User: bioinfo20014

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bioinfo2001410
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Posts by bioinfo20014

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Comment: C: How to use RUVSeq in clustering problems?
... Thanks for your reply. I'm actually using the DESeq2 normalized counts, not rlog, unlike I said. I also tried using raw counts and the betweenLaneNormalization function but got similar results. I am going to try what you suggested. ...
written 6 weeks ago by bioinfo2001410
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How to use RUVSeq in clustering problems?
... I have successfully used RUVSeq to correct samples from a "classical" control vs treatment experiment for batch effects using RUVr, RUVg, RUVs and svaseq and all gave similar results, which were satisfactory. Now I want to use RUVSeq in a clustering problem and I understand I can only use RUVs. I ...
clustering ruvseq rna-seq written 6 weeks ago by bioinfo2001410 • updated 6 weeks ago by davide risso490
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Answer: A: about SVA: matrix of corrected expression values
... I once found the function below to do what you want:   # function from https://support.bioconductor.org/p/47350/   cleaningY = function(y, mod, svaobj) {          X = cbind(mod, svaobj$sv)            Hat = solve(t(X)%*%X)%*%t(X)            beta = (Hat%*%t(y))            P = ncol(mod)            cle ...
written 13 months ago by bioinfo2001410

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