User: greg.deakin

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Posts by greg.deakin

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DESeq2 paired design with missing samples and multiple conditions
... Hi, I've got a paired (or blocks really) experiment with the setup like the below. Five blocks and four conditions (A, B, C, D). I want to contrast all vs all (A vs B, A vs C, A vs D and etc.). The Xs in the table below indicate a sample present for each block (I think it's clearer in table format ...
deseq2 missing data paired samples multiple treatments written 13 days ago by greg.deakin0 • updated 13 days ago by Michael Love20k
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Comment: C: DESeq2 1.16.1 : Zero count values re-occurrence of issue 56191?
... Ah, o.k. thanks Mike. I guess it's pretty much an edge case, especially in RNA-seq, and not too difficult for me to correct for. I'll have a look at using LRT. As you guess my data (mostly soil microbiom) might violate a few of the expectations of the DESeq model - it's a bit of an open question h ...
written 11 months ago by greg.deakin0
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DESeq2 1.16.1 : Zero count values re-occurrence of issue 56191?
... Hello - I have an issue with genes (or OTUs in my case) which have zero expression across a condition. Seems to be the same issue as https://support.bioconductor.org/p/56190/#56191 Works as expected (well as I'd expect) in DESeq2 1.10.1 Below are a few of the details model = ~ Block + Treatment ...
deseq2 written 11 months ago by greg.deakin0 • updated 11 months ago by Michael Love20k

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