User: 15958021290

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Comment: C: the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
... Thank you for your kindly advices. Sorry to bother you. ...
written 6 days ago by 159580212900
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Comment: C: the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
... Thank you for your reply! And what do you think of equalLibSize() fucntion using to output so called "normalized count" like this example https://stats.stackexchange.com/questions/165056/tmm-normalization-of-rna-seq-data-in-r-language-using-edger-package ...
written 7 days ago by 159580212900
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the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
... Hi guys, I want to talk about the the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR.And I want get advice from you about my opinion below: firstly, two methods is similar, they calculate respective scale factor at first.And then they should divided by scale factor to nor ...
normalization edger deseq2 written 8 days ago by 159580212900 • updated 7 days ago by Gordon Smyth38k
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Comment: C: how to get normalized count data from edgeR using TMM methods
... Thank you for your comment! Actually I want to talk about the two normalization(MRN and TMM) methods supplied by DESeq2 and edgeR. two methods is similar, they calculate respective scale factor at first.And then they should divided by scale factor, and DESeq2 prodvide counts(dds, normalized=T) to d ...
written 9 days ago by 159580212900
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Comment: C: how to get normalized count data from edgeR using TMM methods
... Thank you for your quickly reply! I read the the source code of cpm() in https://rdrr.io/bioc/edgeR/src/R/cpm.R. And I find when normalized.lib.sizes =T, lib.size <- lib.size*y$samples$norm.factors. and so the cpm=count/(library-size*norm.factors*10^-6) and it actually using the calculated scale ...
written 10 days ago by 159580212900
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how to get normalized count data from edgeR using TMM methods
... Hi there, I know it is a old question about the normalization of count using edgeR TMM methods.And I know using calcNormFactor(DEGList, method = "TMM") to get norm.factors.But how can I get the normalized count matrix using some command.And I know the simple method is using every count to divide th ...
normalization edger written 11 days ago by 159580212900

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