[BioC] Normalizing Affy Almac Xcel Array Data from CEL files
James W. MacDonald
jmacdon at uw.edu
Tue Jan 7 20:53:15 CET 2014
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.
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 Xcelâ„¢ Array for the profiling of FFPE samples provides the only 3â€™ 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 Ã¢â‚¬Ëœpd.xcelÃ¢â‚¬â„¢
> Can someone add library files for this array?
> -- output of sessionInfo():
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>  LC_PAPER=C LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0
>  BiocGenerics_0.4.0 BiocInstaller_1.8.3
> loaded via a namespace (and not attached):
>  affxparser_1.30.2 affyio_1.26.0 Biostrings_2.26.3
>  bit_1.1-11 codetools_0.2-8 DBI_0.2-7
>  ff_2.2-12 foreach_1.4.1 GenomicRanges_1.10.7
>  IRanges_1.16.6 iterators_1.0.6 parallel_2.15.2
>  preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2
>  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.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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