Consultation about combing batches
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Shaowei Wu ▴ 10
@shaowei-wu-6725
Last seen 9.5 years ago
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: http://www.bu.edu/jlab/wp-assets/ComBat/Usage.html. 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 [[alternative HTML version deleted]]
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