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

[Dr Wei Chen]

Thanks Jim! I was able to use makecdfenv to build a cdf package and then use the affy package for summarization as you suggested. Then I encountered a new problem:

> qc.NORM <- qc(data,call.exprs(data,"mas5"))
Error in setQCEnvironment(cdfn) : 
  Could not find array definition file ' xcelcdf.qcdef '. Simpleaffy does not know the QC parameters for this array type.
See the package vignette for details about how to specify QC parameters manually.

So I create the array definition file xcelcdf.qcdef by copying hgu133plus2cdf.qcdef (I did check that all the probe sets in this file exist on this array) and run it again:

> call.exprs(data,"mas5")
Error: NAs in foreign function call (arg 1)

Does that mean this chip is a PM-only chip? How do I proceed for quality control?

Thanks again!

Wei

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at uw.edu] 
Sent: Tuesday, January 07, 2014 2:53 PM
To: Wei Chen [guest]
Cc: bioconductor at r-project.org; Dr Wei Chen
Subject: Re: [BioC] Normalizing Affy Almac Xcel Array Data from CEL files

Hi Wei,

If you want to use oligo, you need to build it yourself, as apparently you need a celfile in addition to the cdf and probe_tab file. See the vignette for the pdInfoBuilder package, starting on page 5.

These are just 3'biased arrays, so you can also use makecdfenv to build a cdf package and then use the affy package for summarization. See the vignette for makecdfenv.

Best,

Jim



On 1/7/2014 2:03 PM, Wei Chen [guest] wrote:
> 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?
>
> Thanks!
>
> Wei
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>   
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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
> --
> Sent via the guest posting facility at bioconductor.org.
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099