[BioC] [XPS] Background computation on single CEL file

cstrato cstrato at aon.at
Fri Jan 20 17:31:04 CET 2012

Dear Thomas,

Since microarrays are used to compare at least two samples, and 
multichip algorithms such as rma require also at least two samples, xps 
will abort if less than two samples are present.

If you compile xps yourself you could in principle disable this feature 
in method XPreProcessManager::Preprocess() (lines 241-243), however this 
is probable not worth the effort, and I do not guarantee that it will 
work. Simply select two CEL-files.

Best regards

On 1/20/12 2:06 AM, thomas sierocinski wrote:
> Dear All, Dear Christian,
> I've used XPS quite extensively to process/analyse human Exon arrays.
> I would like to make some quality control measures on a single CEL file
> but I'm running into trouble at the background computation/correction
> step: apparently the "bgcorrect.rma" does not allow to process one
> sample at a time.
> Here is my function call (integrated in a pipeline):
> data.bg.rma <- bgcorrect.rma(root.data, root.filename,
> filedir=root.path, update=TRUE, select="antigenomic", exonlevel="all",
> verbose=TRUE)
> Here is the output (error):
> Opening file </Data2/thomas/QC.reporting/ROOT_files/singleCEL.root> in
> <READ> mode...
> Opening file </Data2/thomas/QC.reporting/ROOT_files/singleCEL.root> in
> <UPDATE> mode...
> Opening file </Data2/thomas/QC.reporting/ROOT_files/data_singleCEL.root>
> in <READ> mode...
> Opening file </Data2/thomas/QC.reporting/ROOT_files/data_singleCEL.root>
> in <READ> mode...
> Error: At least two trees need to be selected.
> Error in .local(object, ...) : error in rwrapper function ‘BgCorrect’
> Is there any way to get around that problem?
> Thanks in advance.
> Cheers,
> Thomas

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