User: Michael Salbaum

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4 years, 11 months ago
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m**************@pbrc.edu

Posts by Michael Salbaum

<prev • 8 results • page 1 of 1 • next >
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Answer: A: gene set enrichment
... If I may chime in: GSEA does work with pre-sorted gene lists; human gene names were required last time I looked. I found ranking by fold-change alone not to be satisfactory for GSEA, as this ignores the statistics outcome of a differential expression test. Ranking by (-log10(padj))*(log2(ratio)) w ...
written 5.0 years ago by Michael Salbaum80
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sizepower
... Dear All, I wonder if someone could point me towards some guidance using the package 'sizepower'. The archives have not netted much in this regard; the vignette was very useful. I'm doing a prospective power analysis for an array experiment with a matched pair design. I found the function power.m ...
qpcr gui written 5.1 years ago by Michael Salbaum80
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Gene enrichment question
... I'm not a statistician, but interested in the question. Wouldn't it be warranted to ask the question how 'membership' of DE genes in the stem cell gene set would compare to 'membership' in a randomly drawn gene set of the same size as the stem cell set? Fisher's Exact test to evaluate, then bootstr ...
go written 5.3 years ago by Michael Salbaum80 • updated 5.3 years ago by Aliaksei Holik350
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Differential gene expression: EdgeR / DESeq and identifying noise/outliers
... Hi everyone, I am working on a differential gene expression paradigm; n=7, 3’-expression tag sequencing, AB SOLiD5500XL. We look for expression of ~26,000 RefSeq genes; as input, I’m using a bottom-shaved counts table (~16,500 genes), i.e. rows with a total count sum of 12 or less have been trimmed ...
sequencing edger deseq written 5.4 years ago by Michael Salbaum80
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Answer: A: MacOS Package installation problems
... Thanks for the help, I thought it was just me... michael -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Wed 5/30/2012 1:57 PM To: Michael Salbaum Cc: Sean Davis; bioconductor@r-project.org Subject: Re: [BioC] MacOS Package installation problems Hi Michael, On ...
written 5.5 years ago by Michael Salbaum80
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Answer: A: MacOS Package installation problems
... Hi Dan, I tried setting BioC as well as CRAN mirror as suggested. Using source("http://bioconductor.org/biocLite.R") biocLite("DESeq") still directed to the resources listed below, with access problems, and single packages listed as missing. So, I set the BioC mirror to Seattle, the CRAN mirror ...
written 5.5 years ago by Michael Salbaum80
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Answer: A: MacOS Package installation problems
... Got it to work. A bit tedious, loading single packages by hand, but nevertheless. Thanks for the help, Cheers, michael -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Wed 5/30/2012 11:35 AM To: Sean Davis Cc: Michael Salbaum; bioconductor@r-project.org Subject: R ...
written 5.5 years ago by Michael Salbaum80
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MacOS Package installation problems
... Hi everyone, Newbie question: I'm having trouble with package installation on a Mac (OS 10.6.8) > source("http://bioconductor.org/biocLite.R") > biocLite("DESeq") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Warning: unable to access index for ...
biocinstaller written 5.5 years ago by Michael Salbaum80 • updated 5.5 years ago by Chinedu Orekie10

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