Dear Bioconductor Community,

i have 10 CEL files of the primeview PM-only affymetrix array, and i have pre-prossessed and normalized with rma. I would like to perform Present/Absent calls for non-specific intensity filtering, to remove probesets which are consistenly non expressed(i.e. "absent" in more than 5 of the 10 samples). As i cannot install xps due to the fact that is not available to my current R version( i also tried on 32-bit version on my windows 8 but it didnt worked either), i found the function paCalls in the oligo package: which has the option "DABG" or "PSDABG". 

Thus, my main question is that should i use on of the above options with paCalls, or these are inapropriate because in the first place DABG was designed for exon arrays? 

On the other hand, if i would like to perform a more general filtering on mean log-expression, could i use the genefilter package and try something like this: i.e., filter <- pOverA(0.5, log2(100)) ? Or is too strict ??

Just to mention after rma normalization i found a lot of probesets with very low log2 intensity(from 0-2) and some with negative values.

Any suggestion or proposal would be essential !!!

You might consider trying the UPC function in the SCAN.UPC package. It is designed to indicate whether a gene is expressed or not and can be applied to all types of Affymetrix arrays.

Dear Stephen,

after your notification when i simply tried:

object <- SCAN("C:/Users/Efstathios/Desktop/totalcel/*.CEL", outFilePath="myoutput.txt")

but unfortunately it resulted in:

Package 'pd.primeview' was not found in the BioConductor repository.

The 'pdInfoBuilder' package can often be used in situations like this.

Loading required package: pd.primeview

Attempting to obtain 'pd.primeview' from BioConductor website.

Checking to see if your internet connection works...

Package 'pd.primeview' was not found in the BioConductor repository.

The 'pdInfoBuilder' package can often be used in situations like this.

Error in { : 

  task 1 failed - "The annotation package, pd.primeview, could not be loaded."

In addition: Warning messages:

1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :...

i also tried

biocLite("primeview.db")

BioC_mirror: http://bioconductor.org

Using Bioconductor version 3.0 (BiocInstaller 1.16.4), R version 3.1.1.

Installing package(s) 'primeview.db'

Warning message:

package ‘primeview.db’ is not available (for R version 3.1.1) 

Do you think that is a problem due to the recent new version of Bioconductor ?

sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Greek_Greece.1253  LC_CTYPE=Greek_Greece.1253    LC_MONETARY=Greek_Greece.1253
[4] LC_NUMERIC=C                  LC_TIME=Greek_Greece.1253    

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

other attached packages:
[1] simpleaffy_2.42.0   gcrma_2.38.0        genefilter_1.48.1   affy_1.44.0        
[5] Biobase_2.26.0      BiocGenerics_0.12.1

loaded via a namespace (and not attached):
 [1] affyio_1.34.0         affyPLM_1.42.0        annotate_1.44.0       AnnotationDbi_1.28.2 
 [5] BiocInstaller_1.16.4  Biostrings_2.34.1     DBI_0.3.1             GenomeInfoDb_1.2.5   
 [9] IRanges_2.0.1         preprocessCore_1.28.0 RSQLite_1.0.0         S4Vectors_0.4.0      
[13] splines_3.1.1         stats4_3.1.1          survival_2.38-1       tools_3.1.1          
[17] XML_3.98-1.1          xtable_1.7-4          XVector_0.6.0         zlibbioc_1.12.0      
Warning message:
package ‘BiocGenerics’ was built under R version 3.1.2 

In the PrimeView array there are 49975 probesets after normalization. But i perfomed the UPC_Generic_ExpressionSet 

after an initial non-specific intensity filtering, as i had many probesets with very low intensities