User: Michael Imbeault

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Posts by Michael Imbeault

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Answer: A: BiomaRt down?
... I am, but it's been that way for years at least for me (very unstable service). Michael On 20/01/2011 7:02 AM, Paul Geeleher wrote: > Anyone else having trouble with biomaRt and/or http://www.biomart.org/ today? > > Paul. > ...
written 8.9 years ago by Michael Imbeault220
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Comment: C: Detection Above Background (DABG) on Gene Level for Exon and Gene Arrays
... Hello Pascal, I asked the same question to Affy support (which are very responsive) 6 months ago and here is the answer I got (last part is the most relevant): Hello Dr. Imbeault, Thank you for contacting Affymetrix Technical Support. I have attached a paper that you will find useful. As far ...
written 9.2 years ago by Michael Imbeault220
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Answer: A: how to open a SNP data file as large as 500M in Windows OR just extract part of
... You could try http://www.editpadpro.com/ - it opens arbitrary large files, I opened 1 GB text files with it before. Michael On 09/09/2010 11:26 PM, xiangxue Guo wrote: > Hi,there > > Does anybody know how to open a SNP data file as large as 500M in Windows computer? These data are SNPs ...
written 9.2 years ago by Michael Imbeault220
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Answer: A: removal of genes with low expression values
... If you know that a group of genes are not expressed (for example, Y chromosome genes in a female sample, or cell-type / tissue specific genes), you can use the value of those genes to determine your cutoff. It's not really algorithm (MAS or RMA) dependent. Michael On 07/07/2010 6:28 AM, Hernando M ...
written 9.4 years ago by Michael Imbeault220
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Answer: A: GO term enrichment
... Hello, Did you try to just use DAVID as an alternative to BioC? http://david.abcc.ncifcrf.gov/summary.jsp It can do overrepresentation analysis for GO and much more, you should check it out. Just paste your list of gene, choose Agilent gene ID and you`re pretty much set. Of course, it`s a web int ...
written 9.4 years ago by Michael Imbeault220
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Answer: A: tool for drawing interaction network
... Have a look at Gephi (http://gephi.org/) as an alternative to Cytoscape. They have a library to import graphs - python, php, c++ or java. Michael On 20/05/2010 6:06 PM, Hooiveld, Guido wrote: > Dear list, > > Does anyone know of a method (tool), preferably available in BioC, that allows ...
written 9.6 years ago by Michael Imbeault220
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Answer: A: htqPCR question
... Hi everyone, Is there a way to get a changelog of what changed between bioC 2.5 and 2.6 for individual packages? New functions, bugs fixed, etc? The associated documentation of packages I looked at don't seem to include this. Cheers, Michael ...
written 9.6 years ago by Michael Imbeault220
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Comment: C: Reg: PCA in bioconductor
... Hello, Is there a Bioconductor solution to Medline mining? Say, for a given set of affy identifiers, find gene names, their synonyms, and the pubmed count of abstracts cooccurring with a given keyword (such as a disease name)? If not available in Bioconductor, is any other tool available for this? ...
written 9.7 years ago by Michael Imbeault220
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Comment: C: 64-bit R
... Just to report that I've been able to compile affxparser on R win 64 using 1.19.6 from the devel contrib on bioconductor, using mingw64 (specifically, http://sourceforge.net/projects/mingw-w64/files/Toolchains%20targettin g%20Win64/Personal%20Builds/sezero_20100322/mingw-w64-bin_x86_64-mingw _201003 ...
written 9.7 years ago by Michael Imbeault220
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Comment: C: 64-bit R
... Hello, Sorry for the confusion about the two issues, I was under the impression that the build servers I linked to were the 64 bit version, my bad :) I only became aware of the affxparser on 64 bit problem yesterday, and stumbled upon the aroma.affymetrix group. Having not seen a post about it on ...
written 9.7 years ago by Michael Imbeault220

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