User: Tarca Adi Laurentiu

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14 years, 12 months ago
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15 years, 8 months ago
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l*****@rsvs.ulaval.ca

Posts by Tarca Adi Laurentiu

<prev • 10 results • page 1 of 1 • next >
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normalize.loess in affy package
... Hi, I have a question about the function normalize.loess implemented in affy package. Reading the code I understand (perhaps wrong) that the correction of the intensities of probes is done as: lg(Yi)*=lg(Yi)-1/J(Me_i1+Me_i2+...+Me_ij+...+Me_iJ) eq1) where lg stands for log2, Y is the v ...
normalization written 15.0 years ago by Tarca Adi Laurentiu100
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classifyTestsP vs topTable
... Hi everybody, I use limma to analyze a two-color microarrays data set. Using topTable I find say 15 genes with "holm" adjusted p-values less than a given threshold pt=0.05, but if I use classifyTestsP (specifying the same threshold and adjustment method) I obtain much more than 15. Is there any exp ...
limma written 15.0 years ago by Tarca Adi Laurentiu100 • updated 7 months ago by Gordon Smyth38k
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Reading mev files into bioC
... Hi everybody, Is there any bioC package reading TIGR .mev files? Apparently limma and marray does not include this option. If I am about to make a custom function to do this, does anyone know how to deal with negative intensity values, because several .mev output files in my data set produced wit ...
written 15.1 years ago by Tarca Adi Laurentiu100
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affycomp problem
... Hi everyone, I am trying to use the read.dilution function of affycomp library, and I am getting the following error message: "Error in "[.data.frame"(d, , rownames(pData(dilution.phenodata))) : undefined columns selected" Looking at the code of the function I see that it is trying to ...
affycomp written 15.1 years ago by Tarca Adi Laurentiu100 • updated 15.1 years ago by Rafael A. Irizarry2.3k
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bug in maNormMain ?
... Hi, I have a batch of arrays loaded into a marrayRaw object called Apo. The zipped .RData file containing the object is available at http://www.gch.ulaval.ca/ltarca/shares/ApoRaw.zip I am trying a composite normalization with: library(marray) sc2DA <- maNormMain(Apo, f.loc = list(maNorm2D(),ma ...
normalization marray written 15.4 years ago by Tarca Adi Laurentiu100 • updated 15.4 years ago by Jeff Gentry3.9k
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Re: Classification question(Tom R. Fahland)
... >>Date: Thu, 1 Apr 2004 15:47:48 -0800 >>From: "Tom R. Fahland" >>Subject: [BioC] Classification question >>All >>I had a quick question about how you might best solve a classification >>problem. I have some ideas, but wanted to run it by the group to see ...
classification dose written 15.5 years ago by Tarca Adi Laurentiu100
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HOMEDRIVE in R and maImage() troubles
... Hi there, 1) I got the following error when starting R: "Fatal error: invalid HOMEDRIVE". This occurred after disconnecting the Internet connection and restarting the system. This error disappeared after reconnecting it and restarting the system. At the beginning I though that is because the name o ...
written 15.5 years ago by Tarca Adi Laurentiu100 • updated 15.5 years ago by Liaw, Andy360
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Re: Bioconductor Digest, Vol 12, Issue 28
... At 23:09 2004-02-18, you wrote: >Message: 8 >Date: Wed, 18 Feb 2004 16:25:36 -0600 >From: Joyce Gu >Subject: [BioC] Mising data >To: bioconductor@stat.math.ethz.ch >Message-ID: <4033E6B9@webmail.bcm.tmc.edu> >Content-Type: text/plain; charset="ISO-8859-1" > >Hello, ...
normalization written 15.7 years ago by Tarca Adi Laurentiu100
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Re: Bioconductor Digest, Vol 12, Issue 10
... Hi, Is there any known bug in the function maNorm2D() ? I am trying to use it with the swirl data set, but after calling it as: swirl.C<-maNormMain(swirl, f.loc = list(maNorm2D())) the result seems to be a downward shift of all M values with about 10 decades on the log2 scale which is a nonse ...
written 15.7 years ago by Tarca Adi Laurentiu100

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