User: gavinpaulkelly

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Posts by gavinpaulkelly

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Comment: C: high number of DEGs detected using EBSeq-HMM *****UPDATED
... No - I'd say that is unusual in my experience, but so is 10-12k.  It makes me wonder if variance is being (artificially) reduced - is it a real experiment, or are you simulating the data ...
written 11 hours ago by gavinpaulkelly90
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Comment: C: high number of DEGs detected using EBSeq-HMM *****UPDATED
... Not an EBSeq-HMM user here, but nonetheless it would be handy to know how many timepoints (or number of ordinal levels) you have, and how many replicates.  A large number of timepoints offers a large number of non-flat paths, and it wasn't immediately clear how this is dealt with. Maybe do a DESeq2 ...
written 13 hours ago by gavinpaulkelly90
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Answer: A: DESeq pvalue & padj
... It's in the vignette, and in the help page for DESeq - all samples are treated as replicates (i.e. pooling conditions A and B, and any other conditions you have) for the purposes of estimating the dispersions.  This is still done on a gene-by-gene basis, and as dispersion can vary per gene, so can t ...
written 17 hours ago by gavinpaulkelly90
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Answer: A: DESeq2 log fold change estimates for factors with many levels
... results(dds.bacterial.taxa, contrast=c("treatment", "a", "b")) results(dds.bacterial.taxa, name="treatmenta") results(dds.bacterial.taxa, contrast=list(c("treatmenta", "treatmentb"))) The first one is the one that you want - comparing treatment a with treatment b.  The second compares treatment ...
written 2 days ago by gavinpaulkelly90
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Comment: C: DESeq2 log fold change estimates for factors with many levels
... (note - I posted this comment first, before spotting the problem in your initial code) Could you put the first few lines of output from each of the three calls to results you do, as I'd expect the first and third to both show log2 fold change (MAP): treatment a vs b Wald test p-value: treatment ...
written 2 days ago by gavinpaulkelly90
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Comment: C: Volcano plot non-numeric argument error
... hmm, running out of options without seeing the data; try using 'head', 'summary' and maybe 'plot' on the column resEdgeR$table$PValue to see if there's any clues as to where the non-numeric values are creeping in. ...
written 15 days ago by gavinpaulkelly90
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Comment: C: Volcano plot non-numeric argument error
... It's probably down to the capitalisation of the table names - (you had a lower-case v in pvalue), and also you were referencing tab in the creation of tab itself: try tab = data.frame(logFC = resEdgeR$table$logFC, negLogPval = -log10(resEdgeR$table$PValue))   ...
written 15 days ago by gavinpaulkelly90
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Comment: C: Volcano plot non-numeric argument error
... Did you really mean log10("Pval"), rather than log10(tab[,"Pval"]) ? ...
written 15 days ago by gavinpaulkelly90
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Comment: C: Volcano plot non-numeric argument error
... It looks like the 1st column of your data corresponds to  $   : chr  "NMA0001" "NMA0002" "NMA0003" "NMA0004" so you're numeric columns are off by one, is it any better if you try  tab = data.frame(logFC = resEdgeR$table[, 2], negLogPval = -log10(resEdgeR$table[, 5])) ...
written 15 days ago by gavinpaulkelly90
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Comment: C: DESeq2 - differentially expressed genes for each sample
... Could you clarify what you mean by 'each one of my sample' - do the treated and untreated come in pairs, and you're looking for differential genes in each pair (in which case it's unclear how you're going to get 'differentially expressed genes betweem male and female' to be a meaningful comparison). ...
written 15 days ago by gavinpaulkelly90

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Scholar 15 months ago, created an answer that has been accepted. For A: DESeq2 3-fatcor design and different interaction terms

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