Choose file to start with


This app is a wrapper of the exploBATCH, an R package for evaluating and correcting for batch effect in genomic studies.
Please read the following refererence for more details on exploBATCH
Sci Rep. 2017 Sep 7;7(1):10849. doi: 10.1038/s41598-017-11110-6. A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies.
The comBat method is decribed in SVA package. Here we used the parameter option

Upload data file (tsv/csv)



                        

                      

                    

                  

                  

                    

                      

                        

                          

                            

                              
                            

                          

                        

                      

                    

                  

                

                

                  

                    

                      

                        

                          
Data table pre-process

                          

                            
                          

                        

                        

                          

                            

                              

                                
                              

                            

                            

                              

                                
                              

                            

                            

                              

                                
                              

                            

                            

                              

                                

                                  

                                    

                                      

                                    

                                    

                                      

                                    

                                  

                                

                              

                            

                            

                              

                                
                              

                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                                

                                  
                                  
                                

                              

                            

                            

                              

                                
                              

                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                                

                                  
                                  
                                

                              

                            

                            

                              

                                
                              

                            

                            

                              

                                

                                  
                                  
                                

                                	Q vaule is the presence percentage threshold. For example, 0,75 means 75% of presence across all samples
                              

                            

                            

                              

                                
                              

                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                              

                            

                            

                              

                                
                              

                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                                

                                  
                                  

                                    
                                    
                                  

                                

                                

                                  
                                  
                                

                              

                            

                            

                              

                                
                              

                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                                
                                  	This function centers and scales numeric matrix. 
                                  Center means the data(row or column)'s mean is going to be 0. 
                                  Scale is done after centering. Scale is done by divding each value by their standard deviation.
                                  This function is called z-score some elsewhere. 
                                
                              

                            

                            

                              

                                
                              

                            

                            
                            

                          

                          

                            

                            

                            

                            

                              

                                

                                  

                                    
Original Data

                                  

                                  

                                    

                                  

                                

                              

                            

                            

                              

                                

                                  

                                    
Processed Data

                                  

                                  

                                    

                                  

                                

                              

                            

                          

                        

                      

                    

                  

                  

                    

                      

                        

                          
Expression matrix

                        

                        

                          
                            
                            Download table
                          
                          

                        

                      

                    

                  

                

              

              

                

                  

                    

                      

                        

                          
Upload meta file (tsv/csv, required)

                          

                            
                          

                        

                        

                          

                            

                              

                                

                                  
                                

                              

                              

                                

                                  
                                

                              

                            

                            

                              

                                

                                  
                                

                              

                              

                                
                                

                                  
                                  
                                

                              

                            

                          

                          

                            
                            

                              
                              
                            

                            

                              

                            

                          

                          

                            

                          

                          

                          

                        

                      

                    

                  

                

                

                  
                

              

            

          

          

            

              

                

                  

                    

                      

                        

                          

                            
                            

                              

                                
                              

                              

                                
                              

                              

                                
                              

                            

                          

                        

                        

                          

                            

                              

                              

                            

                            

                              

                                
                                

                                  
                                  
                                

                              

                              

                                

                              

                            

                          

                        

                        

                          

                            

                          

                          

                            

                          

                        

                        

                          

                          

                            
                          

                        

                      

                    

                  

                  

                    

                      

                        
                        

                          

                            

                              

                                

                                  
For Exploring mode, the method doing more assessment to decide the numbers of pPC first.
                              The batch effect (before and after correction using two method) can be quantified and visualized by the box plot.
                              Download the data from the download tab.

                                

                                

                                  

                                    

                                      

                                      

                                        

                                          

                                            

                                              

                                                
                                              

                                            

                                            

                                              

                                                

                                                  

                                                    
Resize noninteractive plot

                                                  

                                                  

                                                    

                                                      
                                                      
                                                    

                                                    

                                                      
                                                      
                                                    

                                                    
                                                  

                                                

                                              

                                              

                                                

                                                  

                                                    
Export plot

                                                  

                                                  

                                                    

                                                      
                                                      
                                                    

                                                    

                                                      
                                                      
                                                    

                                                    

                                                      
                                                      
                                                    

                                                    

                                                      
                                                      
                                                    

                                                    
                                                      
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PCA plot is usually used to visual check if there is any obivous batch effects. 
                            Two methods, ComBat and CorrrectBatch (based on probability) are used to do the correction. 
                            You can clearly tell the power of the correction by comparing the PCA plot before and after. 
                            Download the data from the download tab.

                              

                              

                                

                                  

                                    

                                    

                                      

                                        

                                          

                                            

                                              
                                            

                                          

                                          

                                            

                                              

                                                

                                                  
Resize noninteractive plot

                                                

                                                

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  
                                                

                                              

                                            

                                            

                                              

                                                

                                                  
Export plot

                                                

                                                

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  
                                                    
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You can also check the proportion of PCA variations accross all PCs from PCA anlaysis. 
                            There is for sure some variation beteen the two method correction, but usually highly consistent to earch other.
                            

                              

                              

                                

                                  

                                    

                                    

                                      

                                        

                                          

                                            

                                              
                                            

                                          

                                          

                                            

                                              

                                                

                                                  
Resize noninteractive plot

                                                

                                                

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  
                                                

                                              

                                            

                                            

                                              

                                                

                                                  
Export plot

                                                

                                                

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  
                                                    
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The batch effect on each pairs of the pPCs using PPCA analysis for the optimized number of pPCs

                                

                                

                                  

                                    

                                      

                                      

                                        

                                          

                                            

                                              

                                                
                                              

                                            

                                            

                                              

                                                

                                                  

                                                    
Resize noninteractive plot

                                                  

                                                  

                                                    

                                                      
                                                      
                                                    

                                                    

                                                      
                                                      
                                                    

                                                    
                                                  

                                                

                                              

                                              

                                                

                                                  

                                                    
Export plot

                                                  

                                                  

                                                    

                                                      
                                                      
                                                    

                                                    

                                                      
                                                      
                                                    

                                                    

                                                      
                                                      
                                                    

                                                    

                                                      
                                                      
                                                    

                                                    
                                                      
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The batch effect on each pairs of the PCs using PCA analysis for the top 10 PCs

                              

                              

                                

                                  

                                    

                                    

                                      

                                        

                                          

                                            

                                              
                                            

                                          

                                          

                                            

                                              

                                                

                                                  
Resize noninteractive plot

                                                

                                                

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  
                                                

                                              

                                            

                                            

                                              

                                                

                                                  
Export plot

                                                

                                                

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  

                                                    
                                                    
                                                  

                                                  
                                                    
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                                        Download table
                                      
                                      

                                    

                                  

                                

                              

                            

                          

                        

                      

                    

                  

                  

                    
busy, won't be long ...

                    
                  

                  
                

              

            

          

          

            

              

                

                  

                    
About

                  

                  

                    This app is a simple wrapper for the exploBATCH
                    refer to https://github.com/syspremed/exploBATCH for more details
                    

                  

                

              

              

                

                  

                    
Contact

                  

                  

                    Author: Zhibin Ning
                    

                    Email: ningzhibin@gmail.com
                    

                    Suggestions and bug report
                  

                

              

              

                

                  

                    
Acknowledgement

                  

                  

                    
This shiny apps uses:

                    
DT, data.table: to table manipulation and display

                    
shinyBS: for progressing status.

                    
plotly: to make ggplot2 plot more interactive

                    
ggplot2: for a lot of plotting

                    
Of course, shiny, rstudio, htmlwidgets, and many more

                  

                

              

              

                

                  

                    
ChangeLog

                  

                  

                    V0.2: 20180214, add comBat only mode with parameter correction, and UI adjust and a bug fix to increase the speed
                    

                    V0.11: 20180207, a few bug fix and more preprocess options added
                    

                    V0.1: 20180206, app online