User: lassancejm

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lassancejm30
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Posts by lassancejm

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Comment: C: when to apply quantile normalization with voom in limma/voom framework with RNA-
... Very good points, thanks for your advise. ...
written 3.6 years ago by lassancejm30
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Comment: C: when to apply quantile normalization with voom in limma/voom framework with RNA-
... Well, something is possibly going on here. As I wrote previously, I am expecting some heterogeneity in the dataset. More about the samples: they correspond to a particular brain region sampled in males and females of two different genetic backgrounds. So, there is probably some biological noise comi ...
written 3.6 years ago by lassancejm30
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Comment: C: when to apply quantile normalization with voom in limma/voom framework with RNA-
... Thank you for your answer(s) Gordon, and pointing to reference making use to the quantile normalization. I will be more careful about potential outliers (we expect some heterogeneity between the samples here) as well as interactions between the variables tested here, good point. From what I see, I ...
written 3.6 years ago by lassancejm30 • updated 3.6 years ago by Gordon Smyth38k
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when to apply quantile normalization with voom in limma/voom framework with RNA-seq data?
... Hi all,  I'm using voom and limma to analyse RNA-seq data. In general, I have followed the basic instructions regarding RNA-seq analysis presented in the limma manual.  The matrix of read counts is filtered so that I keep genes where cpm>=1 in at least 3 samples. This is done using the followin ...
limma voom rna-seq quantile normalization limma voom written 3.6 years ago by lassancejm30 • updated 3.6 years ago by Gordon Smyth38k

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