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.
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
_._._._._._._._._._._._._._._._._._
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.
>
