User: Richard Friedman

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Posts by Richard Friedman

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Answer: A: RNA-seq differentially expressed gene finding methods
... Dear Son, The t-test assumes a normal distribution, which is appropriate for continous variables. RNAseq data deals with counts (discrete entities). A negative binomial distribution (EdgeR, Deseq) or a mean dependent variance (VOOM) is much more approriate. Also the 3 methods mentioned abov ...
written 4.9 years ago by Richard Friedman80
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crlmm of other software for oncoscan
... Dear Bioconductor List, Can Crlmm be used on Affymetrix Oncoscan arrays? if not, can anly other bioconductor package be used on these arrays? I ask, because software developed by Raphale Irizarry's lab and other academic labs usually is much better than the commerical software recommended b ...
cancer crlmm written 5.1 years ago by Richard Friedman80
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Answer: A: Substitution for edd package
... Dear 594898865, If I understand your questions correctly, Limma is a giid package for what you want to do. AffylmGUI or OneChannelGui aregraphic user interfaces to Limma. Best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Resea ...
written 5.3 years ago by Richard Friedman80
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Error message using arrayweights
... Dear List, I got the following error message in array weights: arrayw<-arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, tol = 1e-10) Error in arrayWeights(gcrmanm, design, method = "genebygene", maxiter = 50, : convergence problem at gene 3021: array weights not est ...
go cancer mouse4302 keggrest written 5.6 years ago by Richard Friedman80 • updated 5.6 years ago by Matthew Ritchie750
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simultaneous use of robust and weighting methods in limma.
... Dear List, Should arrayweights, eBayes(robust=TRUE), and lmFit(...,method="robust") be used simultanenously in Limma? If not should any combination be used together? Thanks and best wishes, Rich Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert I ...
limma robust arrayweights written 5.6 years ago by Richard Friedman80 • updated 4.6 years ago by Gordon Smyth37k
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Answer: A: (adj.p.value & log2FC) or (B.value & log2FC)
... Dear Deb, I used adjusted.p.value (with fdr) <0.05 because it takes multiple tests into account in computing the signficance. If I have fewer than (say) 50 genes I make the fdr more lenient. If more that 1K genes, I filter by the absolute value of log2FC as well. with hopes that the abo ...
written 5.6 years ago by Richard Friedman80

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