Entering edit mode
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"
