sampleInfo csv file for DESeq2 guide

Question

[Parham]

Hi,

In section 2.4.2 of "Beginner's guide to using the DESeq2 package" it is talking about a CSV file to be imported but I couldn't find it anywhere. Does anybody know where to look it up? The line is:

sampleInfo <- read.csv("/path/to/file.CSV")

Thanks!

Answer 1

[Devon Ryan]

This is likely the sample table described in help(DESeqDataSet). It has a minimum 3 columns. The first is the sample name, the second is the file produced by htseq-counts associated with that sample, and the third and subsequent columns are group affiliations (e.g., condition, genotype or gender).