simpleaffy plot error
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Georg Otto ▴ 510
@georg-otto-956
Last seen 10.2 years ago
Dear Bioconductors, since upgrading to R 2.5 and bioconductor 2.0, the plot.qc.stats function of simpleaffy returns an error. I attached the transcript of my session below. Could anybody give me a hint what is going on? Cheers, Georg > Data AffyBatch object size of arrays=712x712 features (18 kb) cdf=Zebrafish (15617 affyids) number of samples=32 number of genes=506944 annotation=zebrafish notes= > qc<-qc(Data) > plot(qc) Error in rbind(c(), (vals[, p3] - vals[, p5])) : invalid subscript > traceback() 7: rbind(c(), (vals[, p3] - vals[, p5])) 6: .getRatios(object) 5: ratios(x) 4: ratios(x) 3: plot.qc.stats(x, ...) 2: plot(qc) 1: plot(qc) > sessionInfo() R version 2.5.0 (2007-04-23) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "datasets" [7] "utils" "methods" "base" other attached packages: zebrafishcdf simpleaffy genefilter survival affy affyio "1.16.0" "2.10.3" "1.14.1" "2.31" "1.14.0" "1.4.0" Biobase "1.14.0"
Survival cdf genefilter simpleaffy Survival cdf genefilter simpleaffy • 1.0k views
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Entering edit mode
Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 10.2 years ago
Hi Georg, This is now fixed in the most recent updates to the devl and release versions. It will appear soon on the downloads page. release: 2.10.31 devl: 2.11.21 Crispin > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Georg Otto > Sent: 22 May 2007 18:36 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] simpleaffy plot error > > Dear Bioconductors, > > since upgrading to R 2.5 and bioconductor 2.0, the > plot.qc.stats function of simpleaffy returns an error. I > attached the transcript of my session below. Could anybody > give me a hint what is going on? > > Cheers, > > Georg > > > > Data > AffyBatch object > size of arrays=712x712 features (18 kb) > cdf=Zebrafish (15617 affyids) > number of samples=32 > number of genes=506944 > annotation=zebrafish > notes= > > > qc<-qc(Data) > > plot(qc) > Error in rbind(c(), (vals[, p3] - vals[, p5])) : > invalid subscript > > > > traceback() > 7: rbind(c(), (vals[, p3] - vals[, p5])) > 6: .getRatios(object) > 5: ratios(x) > 4: ratios(x) > 3: plot.qc.stats(x, ...) > 2: plot(qc) > 1: plot(qc) > > > sessionInfo() > R version 2.5.0 (2007-04-23) > x86_64-redhat-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLA > TE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8 > ;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC > _MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] "splines" "tools" "stats" "graphics" > "grDevices" "datasets" > [7] "utils" "methods" "base" > > other attached packages: > zebrafishcdf simpleaffy genefilter survival > affy affyio > "1.16.0" "2.10.3" "1.14.1" "2.31" > "1.14.0" "1.4.0" > Biobase > "1.14.0" > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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