User: Rob Dunne

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Rob Dunne230
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Posts by Rob Dunne

<prev • 23 results • page 2 of 3 • next >
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inquiry for CDF file
... HI List, I get the error message "AffyGenePDInfoPkgSeed" is not a defined class when I try to use pdInfoBuilder, but this posted example seems to indicate it works for some. James W. MacDonald wrote: > You then have to create a 'AffyGenePDInfoPkgSeed' object which you can > then use to b ...
biocviews pdinfobuilder written 11.2 years ago by Rob Dunne230
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Comment: C: rma subscript out of bounds with Rat Exon data
... Hi Crespin, Crispin Miller wrote: > Hi Rob, > That's curious... > yes. It only happens with my data set. I just tried the Rat exon data set from the Affymetrix site with no problems. > Please can you let us know which versions of the software you're running > with a call to: > & ...
written 11.6 years ago by Rob Dunne230
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rma subscript out of bounds with Rat Exon data
... Hello Bioconductor list, I get an error when I try to rma normalize a data set of Rat Exon 1.0 ST cel files i.e. library(exonmap) library(ratexonpmcdf) # Rat Exon 1.0ST from #http://xmap.picr.man.ac.uk/download/ data<-read.exon(path="/home/bioinfo/RatDiet/",compress=TRUE) data at cdfNam ...
written 11.6 years ago by Rob Dunne230 • updated 11.6 years ago by Crispin Miller1.1k
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library versions problem
... Hi list, I cant reproduce results that I got before. I am fairly sure that it is to do with incompatible versions I am using R 1.8.1 affy 1.3.26 affyPLM 1.0.0 AffyExtensions 0.6-2 which from the history line on Ben Bolstad's page should be OK. Does anyone have any ideas? Also -- Th ...
assign written 15.5 years ago by Rob Dunne230
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rma causes crash
... HI list, I have a data set that seems to cause a problem with rma (and also justRMA) in that it crashes R. I have upgraded to current versions of the software, to see if this fixes it. Unfortunately it doesnt. The data consists of 52 ecoli affy arrays. Does anyone have any suggestions as t ...
affy written 16.0 years ago by Rob Dunne230
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normalizing 133 a and b
... HI list, how are people normalizing 133a and b chips? here is what I am doing. 1) bg.correct.rma2 (so this is per chip) 2) extract the pm values for all chips 3) for each pair (A and B) get the probes in common (168 genes) and make a linear correction factor to to correct the B chip. 4) adjus ...
written 16.1 years ago by Rob Dunne230 • updated 16.1 years ago by Mark Reimers20
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other timimg questions
... Hi list, with the discussion of (gc)rma times, I thought it might be opportune to aske what other people are doing about the speed of loess in bioconductor 1.2. for 54 arrays I get a time of over 4 hours (I stopped the process then). After experimenting with the parameters in the code I ha ...
limma process written 16.3 years ago by Rob Dunne230
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how is cbind meant to work?
... Hi List, how is cbind meant to work? > class(t1) [1] "marrayRaw" > class(t2) [1] "marrayRaw" > temp<-cbind(t1,t2) Error in cbind(...) : cannot create a matrix from these types > also how do I find out information like this? ie getMethods("cbind") gives me some information b ...
written 16.3 years ago by Rob Dunne230 • updated 16.3 years ago by Marcus Davy680
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Repost: marrayNorm 1.1.3 gets stuck
... Hi List, Please excuse the repost. No one responded to my previous post -- and it seems to me to be quite important. The problem is the new marrayNorm 1.1.3 (installed with bioconductor 1.2) -- which seems to get stuck in an endless loop marrayNorm 1.1.3 (installed with bioconductor 1.2) > ...
process written 16.4 years ago by Rob Dunne230 • updated 16.4 years ago by Gordon Smyth39k
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marrayNorm 1.1.3 gets stuck
... Hi list, I am having trouble with bioconductor 1.2, and particularly marrayNorm 1.1.3 which was installed with it. It seems to get stuck in a loop marrayNorm 1.1.1 > unix.time(experiment1.norm<-maNorm(experiment1, norm="loess")) [1] 803.99 29.73 843.40 0.00 0.00 marrayNorm 1 ...
process written 16.4 years ago by Rob Dunne230

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Popular Question 6.9 years ago, created a question with more than 1,000 views. For R matrix size limits and array data

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