paCalls oligo package

headers Juan Fernández Tajes | 24 Sep 2012 17:09

Dear list, 

I would like to use the paCalls from oligo package for filtering probe sets with absence of transcripts. My
data are from Hugene 1.1 st array (Affymetrix) 
My data after reading CEL files is a GeneFeatureSet with 1178100 features and 23 samples 

>data 
GeneFeatureSet (storageMode: lockedEnvironment) 
assayData: 1178100 features, 23 samples 
element names: exprs 
protocolData 
rowNames: 10SE191_2 10SE207 ... 10SE360 (23 total) 
varLabels: exprs dates 
varMetadata: labelDescription channel 
phenoData 
rowNames: 10SE191_2 10SE207 ... 10SE360 (23 total) 
varLabels: Sample_ID INIBIC_ID ... Cluster2 (11 total) 
varMetadata: labelDescription 
featureData: none 
experimentData: use 'experimentData(object)' 
Annotation: pd.hugene.1.1.st.v1 

I called the paCalls function: 

> dabgPS <- paCalls(data, "PSDABG") 

And I obtained a matrix of 257430x23, how can I used this information to filter those probes without
transcript? 

My aim is to obtain an average expression value in only those probes with a "true" transcription. 

Many thanks in advance 

Juan 

my sessionInfo is: 

R version 2.15.1 (2012-06-22) 
Platform: i386-apple-darwin9.8.0/i386 (32-bit) 

locale: 
[1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8 

attached base packages: 
[1] stats graphics grDevices utils datasets methods base 

other attached packages: 
[1] affy_1.34.0 pd.hugene.1.1.st.v1_3.6.0 genefilter_1.38.0 
[4] limma_3.12.1 annotate_1.34.1 multtest_2.12.0 
[7] oligo_1.20.4 oligoClasses_1.18.0 hugene11sttranscriptcluster.db_4.0.1 
[10] org.Hs.eg.db_2.7.1 RSQLite_0.11.1 DBI_0.2-5 
[13] AnnotationDbi_1.18.1 Biobase_2.16.0 BiocGenerics_0.2.0 

loaded via a namespace (and not attached): 
[1] affxparser_1.28.1 affyio_1.24.0 BiocInstaller_1.4.7 Biostrings_2.24.1 bit_1.1-8 
[6] codetools_0.2-8 ff_2.2-7 foreach_1.4.0 IRanges_1.14.4 iterators_1.0.6 
[11] MASS_7.3-20 preprocessCore_1.18.0 splines_2.15.1 stats4_2.15.1 survival_2.36-14 
[16] tools_2.15.1 XML_3.9-4 xtable_1.7-0 zlibbioc_1.2.0 

--------------------------------------------------------------- 
Juan Fernandez Tajes, ph. D 
Grupo XENOMAR 
Departamento de BiologÃa Celular y Molecular 
Facultad de Ciencias-Universidade da CoruÃ±a 
Tlf. +34 981 167000 ext 2030 
e-mail: jfernandezt@... 
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