User: Clémentine Dressaire

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Posts by Clémentine Dressaire

<prev • 12 results • page 1 of 2 • next >
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Should I compute RMA expression measures separately for different treament groups?
... Dear BioC users, I was wondering wether it would not make sense to perform rma normalization on the 2 (or more) conditions we want to compare separately instead of alltogether as usually performed. This questioning comes from the three conditions I currently have to deal with. They clearly di ...
normalization written 7.5 years ago by Clémentine Dressaire120 • updated 7.5 years ago by Wolfgang Huber13k
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annotation package for Schizosacharomyces pombe
... Dear BioC users, I am using GeneChip Yeast Genome 2.0 Array from Affymetrix and I downloaded the associated yeast2.db annotation package from Bioconductor. Unfortunately this package only has annotation for Saccharomyces cerevisiae probes and I am interested in the ones from Schizosacharomyc ...
annotation yeast yeast2 written 7.7 years ago by Clémentine Dressaire120
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creating GO and KEGG gene set collections for E. coli
... Dear BioC users, I would like to perform gene set analysis with gage analysis using the gene I previously selected as differentially expressed in my condition of interest. My first problem is that I am working with E. coli for which I couldn't find neither kegg.gs or go.gs like files. I thus ...
go gseabase gage written 8.6 years ago by Clémentine Dressaire120
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Comment: C: help with makeGOGraph
... OK this was a glaring mistake from mine. I sincerely apologyze for disturbing with such a stupid thing. I promise I'll pay more attention now and think better before asking anything. Sorry, Cl?mentine On Fri, 12 Nov 2010 13:16:01 -0500, Sean Davis wrote: > 2010/11/12 Cl?mentine D ...
written 8.6 years ago by Clémentine Dressaire120
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Comment: C: help with makeGOGraph
... Hello again, I have completely forgotten to copy my session informations... > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 [4] LC_NUMERIC=C ...
written 8.6 years ago by Clémentine Dressaire120
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help with makeGOGraph
... Dear BioC users, I am trying to construct a GOgraph using a gene list (overgenes[,3]) of messengers that I previously identified as overexpressed in the condition I was interested in. I previoulsy used this same gene list to perform hypergeometric tests and it worked well. With makeGOgraph ...
annotation go written 8.6 years ago by Clémentine Dressaire120 • updated 8.6 years ago by Marc Carlson7.2k
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Comment: C: Getting annotation into eset
... Hi Mike, Could ou explain me the difference between the db and "db" you are using? If db is the character vector with the annotation database for your array without the .db extension, then what does db represent? Again thanks for your help, Cl?mentine On Fri, 29 Oct 2010 14:23:00 +0 ...
written 8.6 years ago by Clémentine Dressaire120
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Comment: C: Getting annotation into eset
... Dear BioC users, I performed different hypergometric tests on my data regarding GO terms and KEGG pathways. With GO resukt I can use the probeSetSummary function to retrieve the gene list associated to each significant category. However this function does not work if I apply the HG test using ...
written 8.6 years ago by Clémentine Dressaire120
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Comment: C: ecoli2.db
... Hello again, Here is the outpout of my sessionInfo(): > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_Fran ...
written 8.7 years ago by Clémentine Dressaire120
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Comment: C: ecoli2.db
... Hello Marc, After making sure that ecoli2.db was available in Bioconductor 2.7 released I tried several times today to install the package as follows and got an error message about ecoli2.db availability: source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor. ...
written 8.7 years ago by Clémentine Dressaire120

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