User: Yang WY

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Yang WY0
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Posts by Yang WY

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Comment: C: DESeq2 design matrix choice
... Thanks for your advice! Since the clinial data varies in cases, I use patients id to represent the difference among patients. As you said, I want to find the difference in TP vs NT while controlling for patient baseline for more exact results, so #2 might be better. ...
written 11 weeks ago by Yang WY0
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DESeq2 design matrix choice
... Hi! I've downloaded HTSeq-Counts of 48 patients from TCGA, all of the patients have a NT aliquot and a TP aliquot,I want to find the DEGs of two conditions using DESeq2, `myfactor` is: > head(myfactor) patient tissue 1 1 NT 2 2 NT 3 3 NT ...
deseq2 design matrix written 11 weeks ago by Yang WY0 • updated 11 weeks ago by Michael Love26k
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Different Expression Analysis with EDASeq,DESeq2,edgeR,RUVSeq
... Hi, This is my first post here and I'm new to RNA-Seq data analysis, especially different expression analysis (DEA). I have read some surveys about "the best practise in RNA-Seq analysis". As they said, when working on DEA, first we should normalize the raw counts on GC content, batch effects, lib ...
normalization edger deseq2 ruvg written 11 weeks ago by Yang WY0 • updated 11 weeks ago by Michael Love26k

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