[BioC] Consultation about combing batches

Shaowei Wu nhshw at channing.harvard.edu
Mon Sep 8 04:28:16 CEST 2014

Dear friend,

I'm trying to use your ComBat R script to eliminate batch effect when
combine high-throughput gene expression data from different batches.
However, there is an issue about the R code specified on the website:

This is the error information:

> ComBat('batchall.txt',skip=1,'clinicaldata.txt')
Reading Sample Information File
Reading Expression Data File
Found 3 batches
Found 66 covariate(s)
Error in `[<-`(`*tmp*`, , i, value = c(NA, NA, NA, NA, NA, NA, NA, NA,  :
  subscript out of bounds

Could you kindly advise me what's the problem? Great thanks.

Best regards,

Shaowei Wu

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