User: Emmanuel Levy

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Emmanuel Levy270
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Posts by Emmanuel Levy

<prev • 27 results • page 2 of 3 • next >
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Comment: C: Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't
... Dear Robert, > That depends a bit on the organism you are wanting to use. For those that > are supported by the org.xx.yy.db packages, such as human, > org.Hs.eg > > there are maps in those annotation packages > [9] "org.Hs.egENSEMBL2EG" "org.Hs.egENSEMBLPROT" > [11] " ...
written 11.1 years ago by Emmanuel Levy270
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Comment: C: Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't
... Dear Sean, That was indeed the issue. I tried to upgrade R yesterday but it didn't work and I had (i) to add a CRAN mirror to the list of Ubuntu package repositories. (ii) use aptitude instead of apt-get because apt-get held back the update for some reason. I'm happy to say that the issue is now f ...
written 11.1 years ago by Emmanuel Levy270
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Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't install it because of RCurl)
... Dear list members, I'd like to carry out a GO TERM enrichment analysis based on ENSEMBL IDs and the GOstats package. Though I have problems installing biomaRt, which I reported to the R mailing list, I was wondering how to use GOstats with biomaRt, i.e., what should be specified for the "annotatio ...
go gostats biomart written 11.1 years ago by Emmanuel Levy270 • updated 11.1 years ago by rgentleman5.5k
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Comment: C: Intra variance Vs inter group variance: scared!
... Dear Naomi, Thanks a lot, I guess this is what I was looking for :) Thanks for the summary too. Typically do you know how common it is that INTER and INTRA variations are comparable? Best, Emmanuel On 2/6/07, Naomi Altman wrote: > CyberT compares the experimental noise to the biological &g ...
written 12.7 years ago by Emmanuel Levy270
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AffyQCReport: "I'm sorry, I do not know about chip type" (celeganscdf)
... Hello, I have an error with affyQCReport: Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: celeganscdf Error in plot(qc(object)) : unable to find the argument 'x' in selecting a method for function 'plot' The reason is that the package of the chip I use (celegans) is ...
cdf genefilter affy simpleaffy affyqcreport written 12.7 years ago by Emmanuel Levy270 • updated 12.7 years ago by Crispin Miller1.1k
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Answer: A: Intra variance Vs inter group variance: scared!
... Dear James and Naomi, Thanks for your suggestions. Quality control is not exactly what I am looking for: I would like to compare the experimental noise compared to the "biological signal". I agree that fold change is not a great measure, and of course I use a statisticaly robust method for compar ...
written 12.7 years ago by Emmanuel Levy270
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Intra variance Vs inter group variance: scared!
... Dear All, I've got two conditions and three replicates per condition: A1 A2 A3 B1 B2 B3 To test the INTRA VS INTER group variance, I compared the fold changes within group and between groups: length(which(A1/A2 > 5))=686 length(which(A1/B1 > 5))=708 The fact that this is similar is quite s ...
written 12.7 years ago by Emmanuel Levy270 • updated 12.7 years ago by Naomi Altman6.0k
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Envir. drosgenome1, GENENAME not defined?
... Dear Bioconductor community, I just started working with the drosgenome1 environment. When I try to get the gene names from drosgenome1GENENAME, I only get 5 gene names and 14005 NA values. > table(GN) GN Fas (TNF receptor superfamily member) ...
go drosgenome1 cdf annotate affy written 13.6 years ago by Emmanuel Levy270 • updated 13.6 years ago by Ting-Yuan Liu FHCRC780
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Answer: A: Preprocessing affymetrix data
... Have a look at PMID: 15693945 It's a comparative analysis of many existing method using a defined dataset as a test bed. Emmanuel On 8/9/05, Ingunn Berget wrote: > Hi > This is more of a theory/litterature question than use of BioC. > > I know there are many different methods for qua ...
written 14.2 years ago by Emmanuel Levy270
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ESS, how to stop screen printing of a huge data structure
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20050712/ f7131b88/attachment.pl ...
written 14.3 years ago by Emmanuel Levy270 • updated 14.3 years ago by Adaikalavan Ramasamy1.8k

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