User: Francois Pepin

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60
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New User
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Last seen:
12 years, 8 months ago
Joined:
14 years ago
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f*****@aei.ca

Posts by Francois Pepin

<prev • 6 results • page 1 of 1 • next >
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Answer: A: "automatic association analysis"
... Hi Weiwei, If you want to know if a given set of genes (ie members of the pathway) are behaving differently in a given set of arrays (ie your disease samples), there are a few ways. The basic way to do this would be to use an hypergeometric test (often used in the case of GO), although it can be tr ...
written 12.7 years ago by Francois Pepin60
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Answer: A: vector allocation error
... Hi Ulrich, If you search in the mailing list archive (http://dir.gmane.org/gmane.science.biology.informatics.conductor), you'll see a fair number of posts about this problem. You should look at the just.gcrma function instead. R tends to like making unnecessary copies of large objects, so people h ...
written 12.8 years ago by Francois Pepin60
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Comment: C: automating makeContrasts call in limm
... Hi Gordon, I should mention that the behavior is different with R 2.2, but it still doesn't work. > myContrasts<-c("t1-t2","t1-3","t2-t3") > contrast.matrix<-makeContrasts(myContrasts,levels=design) Error in eval(expr, envir, enclos) : object "myContrasts" not found > traceback() 3 ...
written 13.1 years ago by Francois Pepin60
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Comment: C: problem read.maimage("Agilent") -limma
... On Wed, 2005-27-07 at 10:29 +1000, Gordon Smyth wrote: > The gene names in the AgilentFE export files contain strings such as \0, > which is being matched as the null character. This is not only causing the > file read to terminate premately, it is also causing a crash of R itself > when ...
written 13.7 years ago by Francois Pepin60
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Answer: A: Sending email with limma?
... Hi Gisberto, It's not really Limma's job to do that. It wouldn't be difficult at all to get a simple script running that takes care of them. On a unix-y system, I'd probably just save it to file (write.table does the trick) and then do system() calls to the mail command or something similar. (ass ...
written 14.0 years ago by Francois Pepin60
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Comment: C: multtest dependencies
... Hi Seth, > It would be helpful if you can provide us with some detail on the > error message you are seeing and what the permissions are on the > relevant package library directories. This is what I'm getting: Warning messages: 1: Incorrect permissions to edit package database, /usr/local ...
written 14.1 years ago by Francois Pepin60

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