Entering edit mode
Georg Otto
▴
510
@georg-otto-956
Last seen 11.2 years ago
Dear Bioconductors,
Once more, I am a bit confused about an error linked with the new
ExpressionSet class. What I am trying to do is to apply fitPLM to an
AffyBatch object. First, I generate the AffyBatch object like this:
targets<-new("AnnotatedDataFrame")
pData(targets)<-read.table("Targets.txt", header=TRUE, row.names=2)
Data<-ReadAffy(celfile.path =cel.path,
filenames = sampleNames(targets),
verbose=TRUE)
Then I use fitPLM and get an error:
Pset<-fitPLM(Data)
Error in .Deprecated(msg = EXPRSET_DEPR_MSG) :
unused argument(s) (msg = "The exprSet class is deprecated,
use ExpressionSet instead")
However ?fitPLM tells me:
This function converts an 'AffyBatch' into an 'PLMset' by fitting a
specified robust linear model to the probe level data
And class() confirms that my object is indeed an AffyBatch:
class(Data)
[1] "AffyBatch"
attr(,"package")
[1] "affy"
I think I am working with the last versions of the needed libraries
(see below). They were updated from the devel repository from
source. Any hints?
Best,
Georg
sessionInfo()
R version 2.4.0 (2006-10-03)
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"
"utils"
[7] "datasets" "methods" "base"
other attached packages:
zebrafishcdf affyPLM gcrma matchprobes affydata
affy
"1.15.0" "1.11.8" "2.7.1" "1.7.1" "1.11.1"
"1.13.12"
affyio Biobase
"1.3.1" "1.13.28"
