[BioC] Normalizing Affy Almac Xcel Array Data from CEL files

Wei Chen [guest] guest at bioconductor.org
Tue Jan 7 20:03:06 CET 2014

I need to normalize Affy Almac Xcel Array Data from CEL files. The following description is quoted from Affy data sheet: "Almac Xcel™ Array for the profiling of FFPE samples provides the only 3’ gene expression array designed and optimized for use with formalin-fixed, paraffin-embedded (FFPE) tissues. This array, offered exclusively through Affymetrix, was designed by Almac for optimal performance in these precious samples."

Looks like the oligo package doesn't have support for this array yet:

> affyRaw <- read.celfiles(celFiles)
Loading required package: pd.xcel
Attempting to obtain 'pd.xcel' from BioConductor website.
Checking to see if your internet connection works...
Package 'pd.xcel' was not found in the BioConductor repository.
The 'pdInfoBuilder' package can often be used in situations like this.
Error in read.celfiles(celFiles) : 
  The annotation package, pd.xcel, could not be loaded.
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘pd.xcel’

Can someone add library files for this array?



 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] oligo_1.22.0        Biobase_2.18.0      oligoClasses_1.20.0
[4] BiocGenerics_0.4.0  BiocInstaller_1.8.3
loaded via a namespace (and not attached):
 [1] affxparser_1.30.2     affyio_1.26.0         Biostrings_2.26.3    
 [4] bit_1.1-11            codetools_0.2-8       DBI_0.2-7            
 [7] ff_2.2-12             foreach_1.4.1         GenomicRanges_1.10.7 
[10] IRanges_1.16.6        iterators_1.0.6       parallel_2.15.2      
[13] preprocessCore_1.20.0 splines_2.15.2        stats4_2.15.2        
[16] tools_2.15.2          zlibbioc_1.4.0       

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