Question

DESeq2 for single gene

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asd • 0

@asd-12785

Last seen 7.0 years ago

I have 950 cases and ~60k genes in a matrix and I would like to test differential expression for one gene. The conditions are true only for that gene.

If the countData parameter of DESeqDataSetFromMatrix function has a matrix only with one row, it doesnt work.

How can I do it?

deseq2 rnaseq • 961 views

ADD COMMENT • link updated 7.0 years ago by Michael Love 41k • written 7.0 years ago by asd • 0

score 0 · Answer 1 · 2017-04-20

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Michael Love 41k

@mikelove

Last seen 52 minutes ago

United States

Can you add more detail? The whole point of DESeq2 is to perform more rigorous testing across many genes by sharing information across those genes (take a look at the DESeq2 paper, and the methods section).

If you only want to test the counts of one gene, you shouldn't use DESeq2.

ADD COMMENT • link 7.0 years ago Michael Love 41k

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If I have ~60k gene and filter the matrix to contain just 10 gene and after that I run DESeq(dds). Does the filtering affect the result of the method?

To clarify the original question: I assume that one gene in my count dataset has different distribution if I consider given cases. I would have liked to know how can I test for this with DESeq2, instead of U-test.

ADD REPLY • link 7.0 years ago asd • 0

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Can you tell me about the 950 cases? And this is RNA-seq? It's important information, to known how to normalize the counts. With 950 cases, afterward you can probably use whatever method you want, e.g. U-test.

ADD REPLY • link 7.0 years ago Michael Love 41k