Help with RSEM counts: do I transpose matrix?
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@0d323187
Last seen 7 days ago
United States

Hello,

Total newbie here. Trying to analyze RNA-seq dataset with RSEM counts from TCGA.

First I need to QC and normalize the dataset. For some reason, rows are patients and columns are genes...confusing. Do I need to transpose first before using something like DESeq2?

Thank you.

RSEM DESeq2 • 332 views
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@james-w-macdonald-5106
Last seen 4 days ago
United States

Yes. Samples in columns and genes in rows.

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Thank you.

If I have questions about QC/normalization, do I ask them here or ask a new question?

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You can ask here, but please read the DESeq2 vignette first, which should answer most questions.

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OK thank you.

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