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Old 10-10-2013, 02:29 PM   #1
Junior Member
Location: Baltimore

Join Date: May 2011
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Default Preparing text files with counts for DESeq2

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.
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Old 10-10-2013, 02:47 PM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

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.
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Old 10-12-2013, 02:42 AM   #3
Simon Anders
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Location: Heidelberg, Germany

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