[BioC] fRMA for Gene ST arrays

[maria]

> 
> 
> 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