[BioC] xps scheme building

[cstrato]

Dear Iain,

Everything is ok, this is just a note (and not a warning message) where 
I list the columns from the Affymetrix annotation file(s) which have 
somehow changed or were deleted by Affymetrix. The reason is that during 
the years Affymetrix has changed/added/deleted columns from their 
annotation files, so this is mainly an information for me.

Best regards,
Christian
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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
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On 6/20/12 5:42 PM, Iain Gallagher wrote:
> Hello List
>
> I have a set of Rat Gene ST CEL files to analyse and have started looking into using xps for this. I have begun by building the required scheme file for the arrays. I have downloaded the relevant files from affymetrix (RaGene-1_0-st-v1.r4.clf,  RaGene-1_0-st-v1.r4.pgf, RaGene-1_0-st-v1.na32.rn4.probeset.csv&  RaGene-1_0-st-v1.na32.rn4.transcript.csv) and built the scheme file as follows:
>
> libdir<- paste(getwd(), 'xpsAnalysis/annotationFiles', sep='/') # the annotation files are here
>
> xps.scheme<- import.exon.scheme('Scheme_RaGene10stv1r4', filedir=paste(getwd(), 'xpsAnalysis/rootScheme', sep='/'), layoutfile = paste(libdir,'RaGene-1_0-st-v1.r4.clf', sep='/'), schemefile = paste(libdir,'RaGene-1_0-st-v1.r4.pgf',sep='/'), probeset = paste(libdir,'RaGene-1_0-st-v1.na32.rn4.probeset.csv', sep='/'), transcript = paste(libdir, 'RaGene-1_0-st-v1.na32.rn4.transcript.csv', sep='/')) # create the scheme
>
>
> Note that I use the import.exon.scheme command as per advice from cstrato for the r4 annotation files (some weblink I can't find just now).
>
>
> This goes well and I get a .root file in the right directory. However I noticed that during the process the following warning is issued:
>
> Importing</.../xpsAnalysis/annotationFiles/RaGene-1_0-st-v1.na32.rn4.probeset.csv>  as<RaGene-1_0-st-v1.anp>...
> Note: The following header columns are missing or in wrong order:
>     <mouse_fl>
>     <mouse_mrna>
>     <rat_fl>
>     <rat_mrna>
>
>
> Something to be concerned about?
>
> I'm not sure what the mouse data would be doing in the annotations for the rat chips but I'm not yet familiar with the platform.
>
> Advice appreciated.
>
> Thanks
>
> iain
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
>   [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8
>   [7] LC_PAPER=C                LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] xps_1.16.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
> 	[[alternative HTML version deleted]]
>
>
>
>
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