Question

DESeq2 for single gene

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asd • 0

@asd-12785

Last seen 7.7 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 • 1.1k views

ADD COMMENT • link updated 7.7 years ago by Michael Love 43k • written 7.7 years ago by asd • 0

score 0 · Answer 1 · 2017-04-20

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Michael Love 43k

@mikelove

Last seen 3 days 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 7.7 years ago Michael Love 43k

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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 7.7 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 7.7 years ago Michael Love 43k