Entering edit mode
Patrick Schorderet
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50
@patrick-schorderet-4037
Last seen 10.2 years ago
Hello everybody,
I wanted to use rMAT for some of my ChIP-chip analysis and tried to
follow the tutorial (http://wiki.rglab.org/index.php?
title=Public:RMAT). I have updated everything (R version 2.11.0 and
rMAT version 2.4.0) and have downloaded the tutorial data file (EM). I
have managed to do everything up to the rbind part. I have the same
summary as in the tutorial (summary(ER)), but as soon as I try to
normalize the data, my R crashes. I am wondering if any of you have
experienced similar outcomes? Could the amount of processing be too
large? Has any of you been able to successfully follow the tutorial?
Thanks for any useful help,
Patrick
R version 2.11.0 (2010-04-22)
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ISBN 3-900051-07-0
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[R.app GUI 1.32 (5573) i386-apple-darwin9.8.0]
> library(rMAT)
Le chargement a n?cessit? le package : IRanges
Attachement du package : 'IRanges'
The following object(s) are masked from 'package:base':
cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
rbind, rep.int,
table
Le chargement a n?cessit? le package : Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Attachement du package : 'Biobase'
The following object(s) are masked from 'package:IRanges':
updateObject
Le chargement a n?cessit? le package : affxparser
> bpmapA<-"P1_CHIP_A.Anti-Sense.hs.NCBIv35.NR.bpmap"
> celA<-c("MCF_ER_A1.CEL","MCF_ER_A3.CEL", "MCF_ER_A4.CEL",
"MCF_INP_A1.CEL", "MCF_INP_A3.CEL","MCF_INP_A4.CEL")
> ERA<-BPMAPCelParser(bpmapA, celA, seqName="chr2")
> bpmapB<-"P1_CHIP_B.Anti-Sense.hs.NCBIv35.NR.bpmap"
> celB<-c("MCF_ER_B1.CEL","MCF_ER_B3.CEL", "MCF_ER_B4.CEL",
"MCF_INP_B1.CEL", "MCF_INP_B3.CEL","MCF_INP_B4.CEL")
> ERB<-BPMAPCelParser(bpmapB, celB, seqName="chr2")
> bpmapC<-"P1_CHIP_C.Anti-Sense.hs.NCBIv35.NR.bpmap"
> celC<-c("MCF_ER_C1.CEL","MCF_ER_C3.CEL", "MCF_ER_C4.CEL",
"MCF_INP_C1.CEL", "MCF_INP_C3.CEL","MCF_INP_C4.CEL")
> ERC<-BPMAPCelParser(bpmapC, celC, seqName="chr2")
>
>
> ER<-rbind(ERA,ERB,ERC)
>
> summary(ER)
Genome interrogated: P1_CHIP_A.Anti-Sense.hs.NCBIv35.NR
P1_CHIP_B.Anti-Sense.hs.NCBIv35.NR P1_CHIP_C.Anti-Sense.hs.NCBIv35.NR
Chromosome(s) interrogated: chr21, chr22
Sample name(s): MCF_ER_A1 MCF_ER_A3 MCF_ER_A4 MCF_INP_A1
MCF_INP_A3 MCF_INP_A4
The total number of probes is: 1015922
Preprocessing Information
- Transformation: log
- Normalization: none