User: hermidalc

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hermidalc0
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Posts by hermidalc

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Comment: C: Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
... But isn’t it true that the `tximport` `countsFromAbundance` options `scaledTPM` and `lengthScaledTPM` are not the same as regular TPM? I remember the quote from Dr . Smyth you mentioned but he was referring to attempting to do DE using regular TPMs as this is only a within sample normalization meth ...
written 8 days ago by hermidalc0
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Comment: C: Multiple samples per individual and unbalanced number of samples per individual:
... I apologize for appearing to be contradictory. It wasn't meant that way. My colleague and I just didn't know in detail how `duplicateCorrelation` works and that it actually compensated for the imbalance. We didn't believe an imbalance in and of itself would bamboozle the analysis, just though if ...
written 11 days ago by hermidalc0
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Comment: C: Further clarification on when not to use duplicateCorrelation with technical rep
... FYI by definition biological samples from different individuals/subjects are also biological replicates. If you have e.g. multiple biological samples per subject then that is a repeated measures design that you would use `duplicateCorrelation` on. A repeated measures design is any where you have m ...
written 11 days ago by hermidalc0
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Comment: C: Multiple samples per individual and unbalanced number of samples per individual:
... Dear Dr Smyth - thanks very much for the answers and advice, particularly regarding the modeling of batch in this repeated measures design. I will look at MDS plots to see how the data clusters. I have two additional follow-up questions, and sorry in advance for many questions but hopefully these ...
written 11 days ago by hermidalc0
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Comment: C: dream vignette says limma-voom repeated measures two-group comparison needs two
... Thank you very much, that makes complete sense. Apologies for not finding it when I searched. ...
written 12 days ago by hermidalc0
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Comment: C: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
... Thank you for the explanation. Oh ok, so scaledTPM and lengthScaledTPM values are equivalent to gene-level quantification read counts? Similar to what would be produced by HTSeq or featureCounts? ...
written 12 days ago by hermidalc0
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Comment: C: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
... Dear Michael - are scaledTPM and lengthScaledTPM values comparable across samples? (which TPM is definitely not) I could be completely mistaken, but while both adjust for library size and gene length neither adjust for RNA/library composition? (like DESeq2 median of ratios and edgeR TMM normalizatio ...
written 12 days ago by hermidalc0
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Comment: C: dream vignette says limma-voom repeated measures two-group comparison needs two
... Very sorry, I do usually read the return value description I simply forgot in this case. Thank you for the help! ...
written 12 days ago by hermidalc0
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Comment: C: dream vignette says limma-voom repeated measures two-group comparison needs two
... Thank you both James and Gabriel. It's much clearer now. ...
written 12 days ago by hermidalc0
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Comment: C: dream vignette says limma-voom repeated measures two-group comparison needs two
... My apologies yes I found that phrase confusing, since I thought it meant that passing `block` and `correlation` options to `voom` would mean they weren't actually used there and simply passed to the subsequent call of `lmFit(v, ...)` with the `voom` result so you wouldn't need to specify `block` and ...
written 12 days ago by hermidalc0

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