User: cmfield

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cmfield0
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Posts by cmfield

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Comment: C: Handling multiple knockout experiments with DESeq2
... Well, to be precise, I'm saying 'genes' when I mean 'countable things' because it's not RNASeq data, which is one of the reasons why I have very low numbers of countable things > 10. I didn't want to complicate the original post but more understand the theory. I have so far constructed sub-tables ...
written 6 months ago by cmfield0
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Comment: C: Handling multiple knockout experiments with DESeq2
... It's approximately the same set in each condition (other than some that go from <10 to >10 in a knockout), of 50-100. ...
written 6 months ago by cmfield0
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Comment: C: Handling multiple knockout experiments with DESeq2
... On the order of 100 I would say, not so many. I suppose another way to look at it is.. is it worth separating the knockouts into different analyses at the cost of less robust size factor estimation? ...
written 6 months ago by cmfield0
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Handling multiple knockout experiments with DESeq2
... This is a sanity-check question about how I ought to correctly use DESeq2 with knockout experiments. If I have two conditions, a control and a knockout, am I correct in putting them into one data set and then later ignoring the specific result for the knocked-out gene? I would guess that should a no ...
deseq2 written 6 months ago by cmfield0 • updated 6 months ago by Michael Love24k
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Do I have too many samples or are some samples causing issues?
... I have RNASeq count data from 42 different conditions, 5 repeats per condition for a total of 210 samples, and approximately 37,000 genes. DESeq freezes up at the estimateDispersions step unless I slice the data down to ~50 samples or so. Is it the case that the calculation time scales up in the ext ...
deseq2 written 7 months ago by cmfield0 • updated 7 months ago by Michael Love24k

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