[BioC] Custom CDF for alternative splicing with xps

[cstrato]

Hi,

For expression arrays xps does support alternative arrays from 
BrainArray. For this purpose function rma has the parameter 
'xps.scheme', see ?rma and ?import.expr.scheme

In principle you can do:
# HuEx-1_0-st-v2.r2: BrainArray Version 16
scheme.huex10stv2ENSE <- import.expr.scheme("huex10stv2ENSE", filedir = 
scmdir,
                               schemefile = file.path(libdir, 
"HuEx10stv2_Hs_ENSE.cdf"),
                               probefile  = file.path(libdir, 
"HuEx10stv2_Hs_ENSE_probe.tab"),
                               annotfile  = "",
                               chipname   = "HuEx-1_0-st-v2_umi16_ense")


However this scheme file will not help you since for whole genome arrays 
xps does only support pgf-files and no cdf-files, so it can not use the 
alternative cdf-files provided by BrainArray.

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
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On 12/6/12 5:58 PM, Binbin [guest] wrote:
> Hello there, using xps and affymetrix official PGF files, I have built a scheme for hs exon_st1.0_v2 analysis at the transript level. Now we want to study isoforms by looking at the data at the exon level. One issue we want to avoid is the multiple-mapping of same probes and a reasonable up-to-date annotation. Brainarray's custom CDF (v16 Ensembl exon) seems a good choice. My question is - can import.expr.scheme() in xps build a root using these custom CDF files? Have gone through the xps reference/manual but still not sure.
> Many thanks for suggestions.
>
>
>   -- output of sessionInfo():
>
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
>   [7] LC_PAPER=C                LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] xps_1.18.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>