Question: DESeq2 for single gene
gravatar for asd
9 days ago by
asd0 wrote:

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?

ADD COMMENTlink modified 9 days ago by Michael Love11k • written 9 days ago by asd0
gravatar for Michael Love
9 days ago by
Michael Love11k
United States
Michael Love11k wrote:

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 COMMENTlink written 9 days ago by Michael Love11k

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 REPLYlink written 9 days ago by asd0

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 REPLYlink written 9 days ago by Michael Love11k
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