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maria
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@maria-6339
Last seen 10.3 years ago
>
>
> Kamila,
>
> You can preprocess Gene ST arrays using the latest version of frma
--
> just load the data using the oligo package. And you can obtain GNUSE
> values using the GNUSE function on the preprocessed data object.
>
> A barcode implementation for the Gene ST arrays is not currently
> available, but it is in the works -- hopefully it will be ready
before
> the fall BioC release.
>
> Best,
> Matt
>
> On Wed, Apr 3, 2013 at 8:41 AM, Naxerova, Kamila
> <naxerova at="" ...=""> wrote:
> > Dear list,
> >
> > to preprocess Affymetrix whole transcript arrays, use of oligo and
xps
is recommended over the affy
> package. I am interested in using the GNUSE algorithm to assign
quality
scores to some arrays, and would
> also like to try out the barcode function in the frma package. I am
now
wondering... is frma compatible with
> whole transcript arrays?
> >
> > Thanks a lot.
> > Kamila
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at ...
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
Hi,
First, I apologize if I posted this message at the wrong place. I
tried to
run barcode for the hugene.1.0.st.v1 and got an output for only 4000
probes.
The problem seems that when barcode maps the probe names from
"hugene.1.0.st.v1frmavecs" to my data the overlap is only of 4000
although
tau and mu contains about 37000 items. I wonder if I did a mistake in
my
coding (I'm new in microarray analysis) or if this is really what
happens.
(see script below). I also tried to edit the code of barcode to add a
new
platform and I assigned the vector hugene.1.0.st.v1frmavecs to the
pkg.
(pkg <- "hugene.1.0.st.v1frmavecs") but it does not help.
Thank you in advance for your help
Maria
library("oligo")
library(pd.hugene.1.0.st.v1)
celFiles = list.celfiles()
affyRaw= read.celfiles(celFiles)
library("hugene.1.0.st.v1frmavecs")
data("hugene.1.0.st.v1frmavecs")
data("hugene.1.0.st.v1barcodevecs")
library("frma")
eset=frma(affyRaw,input.vecs=hugene.1.0.st.v1frmavecs,
summarize="median_polish" )
b=barcode(exprs(eset),platform=NULL,mu=hugene.1.0.st.v1barcodevecs$mu,
tau=hugene.1.0.st.v1barcodevecs$tau, output="p-value")
R version 2.15.2 (2012-10-26)
Platform: i386-w64-mingw32/i386 (32-bit)
attached base packages:
[1] stats graphics utils methods base
other attached packages:
[1] frma_1.10.0 hugene.1.0.st.v1frmavecs_1.0.0
[3] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.4
[5] DBI_0.2-7 oligo_1.22.0
[7] Biobase_2.18.0 oligoClasses_1.20.0
[9] BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] affxparser_1.30.2 affy_1.36.1 affyio_1.26.0
[4] BiocInstaller_1.8.3 Biostrings_2.26.3 bit_1.1-11
[7] codetools_0.2-8 ff_2.2-12 foreach_1.4.1
[10] GenomicRanges_1.10.7 grDevices_2.15.2 IRanges_1.16.6
[13] iterators_1.0.6 MASS_7.3-23 parallel_2.15.2
[16] preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2
[19] tools_2.15.2 zlibbioc_1.4.0
