## User: hermidalc

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#### Posts by hermidalc

<prev • 14 results • page 1 of 2 • next >
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... 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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... 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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... 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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154
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... 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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... 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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... 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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... 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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102
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... 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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102
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... Thank you both James and Gabriel. It's much clearer now. ...
written 12 days ago by hermidalc0
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... 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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