Preparing text files with counts for DESeq2

[KHubbard]

All, we have been using DESeq for about a year now, and would like to compare our results to DESeq2.

We have been using raw count files in text format. What are the commands to convert a text files (.csv) to a format readable by DESeq2? This may be obvious to experienced R users, but has us at a complete loss.

Our files contain gene names in column 1 and sample names (biological replicates, 4 for each experimental condition) in row 1. Gene names are not duplicated and counts are in integers.

[dpryan]

The formats are (or at least can be) the same for both DESeq and DESeq2. Just use read.csv() as you would for any other CSV file.

[Simon Anders]

"DESeqDatasetFromMatrix" is the function you want to use instead of "newCountDataset"