[BioC] xps library with mouse gene 1.0 transcript arrays

[cstrato]

Dear Assa,

I assume that you get the error since you are mixing MoGene-1_0-st 
pgf-files with MoGene-2_0-st annotation files.

For MoGene-2_0-st you need to do:

scheme.mogene20st.na33 <- import.exon.scheme("mogene20stv1", filedir = 
file.path(scmdir, "na33"),
    file.path(libdir, "MoGene-2_0-st", "MoGene-2_0-st.clf"),
    file.path(libdir, "MoGene-2_0-st", "MoGene-2_0-st.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"))

For MoGene-1_0-st arrays you would need the MoGene-1_0-st annotation files.

Furthermore, your version of xps is pretty old, even for R-2.15.x. I 
would suggest to update to the latest versions of R and xps.

Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._


On 9/23/13 3:02 PM, Assa Yeroslaviz wrote:
> 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