User: Michael Salbaum
Michael Salbaum • 80
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- 5 years, 7 months ago
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- 6 years, 1 month ago
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Posts by Michael Salbaum
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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 5.6 years ago by
Michael Salbaum • 80
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... 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 ...
written 5.8 years ago by
Michael Salbaum • 80
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... 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 ...
written 5.9 years ago by
Michael Salbaum • 80
• updated 5.9 years ago by
Aliaksei Holik • 350
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... 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, Im using a bottom-shaved counts
table (~16,500 genes), i.e. rows with a total count sum of 12 or less
have been trimmed ...
written 6.1 years ago by
Michael Salbaum • 80
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... 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 6.1 years ago by
Michael Salbaum • 80
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... 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 6.1 years ago by
Michael Salbaum • 80
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... 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 6.1 years ago by
Michael Salbaum • 80
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... 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 ...
written 6.1 years ago by
Michael Salbaum • 80
• updated 6.1 years ago by
Chinedu Orekie • 10
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