User: Celine Carret

gravatar for Celine Carret
Celine Carret220
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10 years, 8 months ago
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13 years, 10 months ago
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c**@sanger.ac.uk

Posts by Celine Carret

<prev • 22 results • page 2 of 3 • next >
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Comment: C: [SAGEnhaft] This library does all post analysis on SAGE or is need another softw
... Sure, sorry: thank you C. >list <- read.table("list.txt", sep="") > class(list) [1] "data.frame" >list <- as.matrix(list) > intersect(exprs(eset), list) character(0) >intersect(exprs(eset), as.character(list)) character(0) >exprs(eset)[list] [1] NA NA NA NA ... ...
written 12.9 years ago by Celine Carret220
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Answer: A: [SAGEnhaft] This library does all post analysis on SAGE or is need another softw
... Hi, I'm stuck remembering the way of subsetting an eset object (19 affy arrays) to accomodate only a defined list of genes that I'm interested in. I read.table(list) into R, transformed it as.matrix and use the functions: exprs(eset)[list] or exprs(eset)[as.character(list)] those functions recogniz ...
written 12.9 years ago by Celine Carret220
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Answer: A: [Fwd: Re: RBGL1.8 on 64bit Linux?]
... Hi, problem solved using a newer version of g++ Thanks so much for your help and advices Celine Li.Long at isb-sib.ch wrote: >Here's what I have on my machine: >$ uname -a >Linux devfrt01.vital-it.ch 2.6.9-22.0.1.EL_SFS2.1_0 #1 SMP Thu Feb 9 >17:18:32 CET 2006 ia64 ia64 ia64 GNU/Linux ...
written 13.2 years ago by Celine Carret220
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[Fwd: Re: RBGL1.8 on 64bit Linux?]
... Hi, here are the info: >> (1) what's g++ version? (you could find out by: g++ --version ) > > > g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-42) > >> (2) it seems you installed through some job queue, what do you get when >> you do it manually: .../R CMD INSTAL ...
written 13.2 years ago by Celine Carret220 • updated 13.2 years ago by Li.Long@isb-sib.ch510
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Comment: C: RBGL1.8 on 64bit Linux?
... I have copied the error message on this .txt file. I hope this will help... Best wishes Celine Li.Long at isb-sib.ch wrote: >I have no problem building the package on IA-2 64bit machine w/ gcc and icc. >If you could provide us the error msgs you got from your installation, >we have a cha ...
written 13.2 years ago by Celine Carret220
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RBGL1.8 on 64bit Linux?
... Dear List, When trying to install RBGL1.8 for R-2.3.0 on Linux Itanium2 machines (64bit), it doesn't compile, giving pages of error messages, while it does compile on similar machines (same compiler) but 32 bit. Does someone have an idea why this doesn't compile on a 64? the package was downloaded ...
written 13.2 years ago by Celine Carret220 • updated 13.2 years ago by Li.Long@isb-sib.ch510
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plotting GO output as pie charts
... Hi everybody, I was wondering if there was a simple function allowing me to do this, plotting a GO-output search from ensembl into a pie-chart? I looked at biomaRt but the main problem I'm facing here is actually calling ensembl database as my Institute doesn't allow me to do so through R (I'm worki ...
go biomart written 13.3 years ago by Celine Carret220 • updated 13.3 years ago by Dick Beyer1.4k
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affy scalevalue for RMA?
... Dear list, I'm trying to better understand what the "affy.scalevalue.exprSet" function does exactly (affy package). I know it is normally used for MAS pre-processing, but I found it very useful in an RMA context, to kind of normalise different set of chips to the same "subset" that has been median ...
written 13.5 years ago by Celine Carret220
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Comment: C: (Limma) different toptable results for the same dataset using 2 different design
... Dear gordon, thank you very much for your answer. However, when I do that, I end up with the table below: >>Here is what I've done: >> > design2 <- cbind(A=1, BvsA=c(0,0,1,1)) >> > fit2 <- lmFit(eset, design2) >> > fit2eB <- eBayes(fit2) >> > topta ...
written 13.7 years ago by Celine Carret220
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Answer: A: custom PM only chips and CDF files
... Hi Stephen, I have been working with PM-only custom Affy chips for few years now and working with R has never been a problem. You need to create a special environment or package using your CDF, and some of the affy function will not be available to you, but it isn't so much of a big deal. Best wis ...
written 13.7 years ago by Celine Carret220

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Popular Question 10.7 years ago, created a question with more than 1,000 views. For Extracting genes within venn diagram

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