User: ginlucks

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ginlucks0
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Posts by ginlucks

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Handling batch effect with Limma
... Hi everybody, I read a lot of threads but probably I miss the right one...anyway here is my question: I have an expression matrix (expressionData) with 2 different conditions: HLT and TUM These two conditions derives from aggregating data from 3 different experiments (which use different platform ...
limma batch effect batch effect correction written 4 months ago by ginlucks0 • updated 4 months ago by Gordon Smyth37k
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Comment: C: use tximport's countsFromAbundance when using DESeq2
... Thanks for answer   ...
written 16 months ago by ginlucks0
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use tximport's countsFromAbundance when using DESeq2
... Hi all, I was wondering if using tximport to import salmon qf files I have to use the countsFromAbundance option (it is meant to score counts using abundance estimates scaled up to library size) since DESeq2 uses un-normalized data and since by the "counts" function it is possible to get normalized ...
rnaseq normalization deseq2 salmon tximport written 16 months ago by ginlucks0 • updated 16 months ago by Michael Love24k

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