DESeq2 data input
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zhaoy • 0
@zhaoy-23696
Last seen 14 months ago

Enter the body of text here Instead of raw count data, would it be proper to input the normalized RNAseq count data into DESeq2? The TCGA RNASeqV2 data is downloaded from cbioportal. From the reference, it seems they normalized "raw_count" (expected count from RSEM) values by the 75th percentile of the column (after removing zeros) and multiply that by 1000. Would you see any problems by doing that? Thanks for your comments!

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DESeq2 • 254 views
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@mikelove
Last seen 3 hours ago
United States

This has been asked before. No, DESeq2 really requires count data.

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Hi Michael,

I recently ran DESeq2 with TCGA data. I initially used the normalized z scores for DESeq2 but it did not accept negative values. I then used the data from the RNA_Seq_v2_expression_median.txt file and it worked. I was wondering if this is the count data and if it's ok to use? Thanks!

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I don't know -- there have been approximately one hundred posts on the support site about running DESeq2 on TCGA though :-) See the right sidebar.

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