User: Richard Friedman

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Posts by Richard Friedman

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Comment: C: ANCOVA microarray time-course continuous & categorical variables / Limma extensi
... On Oct 22, 2013, at 5:30 PM, Michael Breen wrote: > Hi all, > > Our lab analyzes gene-expression from microarray and RNAseq platforms. > Currently, I am looking for a package to test differential expression (DE) > while considering continuous variables that may alter gene- expressio ...
written 4.1 years ago by Richard Friedman2.0k
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Comment: C: ANCOVA microarray time-course continuous & categorical variables / Limma extensi
... On Oct 22, 2013, at 5:30 PM, Michael Breen wrote: > Hi all, > > Our lab analyzes gene-expression from microarray and RNAseq platforms. > Currently, I am looking for a package to test differential expression (DE) > while considering continuous variables that may alter gene- expressio ...
written 4.1 years ago by Richard Friedman2.0k
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fdr cutoff
... On Oct 1, 2013, at 3:16 AM, Smeeta shrestha wrote: > Dear Dr Friedman, > > I am keen to know the cut off for Adjusted- pvalue . I saw your post to Delasa.(I have attached the whole post in this email for your reference) > > "Say you use a p-value cutoff <0.05. As long as this val ...
cancer written 4.1 years ago by Richard Friedman2.0k
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Answer: A: p-value vs adjusted p-value in DEXSeq
... On Jun 19, 2013, at 1:10 PM, Delasa Aghamirzaie wrote: > Hi, > I have used DEXSeq for differential exon usage testing. I believe what > DEXSeq uses as threshold for finding significant differentially expressed > exons is p-adjust < 0.1 and it reports both p-value and p-adjust in its ...
written 4.4 years ago by Richard Friedman2.0k
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Comment: C: error and warning message with blocked samples with Limma
... On Apr 6, 2013, at 7:41 PM, Gordon K Smyth wrote: > Dear Richard, > > The error is coming when you set colnames for a matrix. When you try to set colnames for matrix, you must give the correct number of names as there are columns in the matrix, and the error is saying that you are not doi ...
written 4.6 years ago by Richard Friedman2.0k
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error and warning message with blocked samples with Limma
... Dear Bioconductor List, I want to do a linear model analysis of a blocked dataset in Limma. I get an error message if I closely follow the manual, or a warning message if I do it a little differentially. I understand from previous posts that the warning message may not be serious, but I wou ...
go cancer mouse4302 limma written 4.6 years ago by Richard Friedman2.0k • updated 4.6 years ago by Gordon Smyth32k
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Comment: C: (no subject)
... On Mar 14, 2013, at 3:04 PM, n omranian wrote: > > Dear Rich, > Thanks a lot for your reply. I will check it and inform you about the result. but nothing exists in R? > Thanks. > Nooshin > Not of which I am aware but maybe someone else on the list knows. Rich ...
written 4.7 years ago by Richard Friedman2.0k
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Comment: C: (no subject)
... Dear Nooshin, I believe that the Metscape 2 add-on to Cytoscape can do what you want. Best wishes, Rich On Mar 14, 2013, at 2:59 PM, n omranian wrote: > Hi, > > Does anybody aware of any package in R or know how we can map metabolites to genes. > I mean all of the enzymatic ge ...
written 4.7 years ago by Richard Friedman2.0k
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Comment: C: QuasiSeq vs DSS
... Dear Ryan, Thank you for your response. 3 questions: 1. If I had just a simple pairwise comparison is it known DSS or QuasiSeq better? 2. I was unaware that an approximate implementation of QuasiSeq was available in edgeR. If so, is it known hor it compare to the ordinairy EdgeR on the one ...
written 4.7 years ago by Richard Friedman2.0k
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QuasiSeq vs DSS
... Dear List. The papers on DSS (included in Bioconductor): Wu H, Wang C, Wu Z. A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data. Biostatistics. 2013 Apr;14(2):232-43. and QuasiSeq (included in CRAN): Lund SP, Nettleton D, McCarthy DJ, Sm ...
rnaseq cancer edger dss written 4.7 years ago by Richard Friedman2.0k • updated 4.7 years ago by Ryan C. Thompson6.1k

Latest awards to Richard Friedman

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Centurion 4.1 years ago, created 100 posts.

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