Hi everybody,

I am trying to work with the xps package on mouse transcript arrays but
having problem creating the root scheme.

This is the command I am using to start with (taken from the scripts given
with the package)

scheme.mogene10stv1.na33 <- import.exon.scheme("mogene10stv1", filedir =
file.path(scmdir, "na33"),
                            file.path(libdir, "MoGene1_0_libFiles",
"MoGene-1_0-st-v1.r4.clf"),
                            file.path(libdir, "MoGene1_0_libFiles",
"MoGene-1_0-st-v1.r4.pgf"),
                            file.path(anndir,
"MoGene-2_0-st-v1.na33.2.mm10.probeset.csv"),
                            file.path(anndir,
"MoGene-2_0-st-v1.na33.2.mm10.transcript.csv"))

But when I am running this command I get the following error massage:
Creating new file
</Users/ayeroslaviz/Documents/Annotations/xps//na33/mogene10stv1.root>...
Importing
</Users/ayeroslaviz/Documents/Annotations/xps//MoGene1_0_libFiles/MoGene-1_0-st-v1.r4.clf>
as <MoGene-1_0-st-v1.cxy>...
   <1102500> records imported...Finished
New dataset <MoGene-1_0-st-v1> is added to Content...
Importing
</Users/ayeroslaviz/Documents/Annotations/xps/MoGene1.0_Annotations//MoGene-2_0-st-v1.na33.2.mm10.probeset.csv>
as <MoGene-1_0-st-v1.anp>...
Note: The following header columns are missing or in wrong order:
   <mouse_fl>
   <mouse_mrna>
   Number of probesets is <269751>.
   <269751> records read...Finished
   <269049> records imported...Finished
   <215654> exon annotations imported.
Importing
</Users/ayeroslaviz/Documents/Annotations/xps//MoGene1_0_libFiles/MoGene-1_0-st-v1.r4.pgf>
as <MoGene-1_0-st-v1.scm>...
   Reading data from input file...
   Number of probesets is <241576>.
   Note: Number of annotated probesets <269751> is not equal to number of
probesets <241576>.
   <241576> records read...Finished
   Sorting data for probeset_type and position...
   Total number of controls is <45>
   Filling trees with data for probeset type: control->chip...
   Number of control->chip items is <0>.
   Filling trees with data for probeset type: control->bgp...
   Filling trees with data for probeset type: control->affx...
   Number of control->affx probesets is <21>.
*Error: Number of control->affx imported <21> is not equal to number of
annotated AFFX controls <167>.*
*Error: CDF with version/magic number
</Users/ayeroslaviz/Documents/Annotations/xps//MoGene1_0_libFiles/MoGene-1_0-st-v1.r4.pgf>
is not supported.*
*Error in import.exon.scheme("mogene10stv1", filedir = file.path(scmdir,  :
  error in function ‘ImportExonSchemes’*

I would like to know what I am doing wrong and how to do it right, so that
the scheme will be uploaded into R with the right annotation files.

Thanks

Assa

I'm working on MacBook Pro 10.7.5
R session info -
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Biobase_2.16.0      BiocGenerics_0.2.0  xps_1.16.0
[4] BiocInstaller_1.4.9

loaded via a namespace (and not attached):
[1] tools_2.15.0

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