There are two line 216 and 218 Three development stages 5 WEEK (5W), 7W, 9W.
Three tissue: Ca, Co, Pa each with 2 biological replicate. With two biological replicate. I want to do differential gene expression analysis using DESeq2 so I tried these codes after reading about DESeq2: ,my aim is to do the pairwise comparison. how to make colData and design formula. library("DESeq2") countMatrix = read.table("read_count.22May.2017.new.txt",header=T,sep='\t',check.names=F) head(countMatrix) dim(countMatrix) [1] 57894 35 Now I am not sure how to construct a DESeqDataSet: dds <- DESeqDataSetFromMatrix(countData = countMatrix, colData = colData, design = ~ condition) Thanks Yogesh -- *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological Science* *Seoul National University* *Seoul, South Korea* [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.