[BioC] using frma and brainarray cdf on exon arrays

[Steve Piccolo]

Hi Ty,

The exon arrays have about 5 million probes. By default, the oligo package
uses only a subset of these probes, which have been flagged as being most
useful. However, the BrainArray package may want to include probes that
are not included by oligo. Thus it may be valuable to start with all
probes (exonarrayTarget=³probeset²) so that all probes included in the
BrainArray mappings will be included. The previous version of SCAN.UPC
uses the default oligo probes.

Regards,
-Steve

On 1/14/14, 7:27 AM, "Ty Thomson" <tthomson at selventa.com> wrote:

>Hi Steve,
>
>Thanks for the suggestion.  I'm running bioconductor 2.12 with
>SCAN.UPC_2.0.2, and it doesn't look like this version of SCAN supports
>the exonArrayTarget parameter.  After reading the documentation for the
>exonArrayTarget parameter in the most recent version of SCAN I don't
>really understand exactly what it does.  Can you give me a bit more
>information on the difference when using a brain array CDF
>(probeSummaryPackage=hgu133plus2hsentrezgprobe) between what happens in
>my current version of SCAN and in the newest version when setting
>exonArrayTarget="probset"?  I am reluctant to change version of
>bioconductor mid-project for the effects this could have on other aspects
>of the project (and the potential need to re-run everything again).
>
>Regards,
>
>Ty
>
>-----Original Message-----
>From: Steve Piccolo [mailto:stephen.piccolo at hsc.utah.edu]
>Sent: Tuesday, January 14, 2014 8:25 AM
>To: bioconductor at r-project.org; Ty Thomson
>Subject: Re: using frma and brainarray cdf on exon arrays
>
>Hi Ty,
>
>Another option is to try the SCAN.UPC package. It is also designed to
>support single-sample normalization. And it should be able to integrate
>the BrainArray annotations for the exon arrays. In the SCAN function, pay
>attention to the probeSummaryPackage and exonArrayTarget parameters. And
>the InstallBrainArrayPackage function may come in handy.  Let me know if
>you run into any troubles with it.
>
>Regards,
>-Steve
>
>
>
>On 1/14/14, 4:00 AM, "bioconductor-request at r-project.org"
><bioconductor-request at r-project.org> wrote:
>
>>Date: Mon, 13 Jan 2014 20:25:44 +0000
>>From: Ty Thomson <tthomson at selventa.com>
>>To: Matthew McCall <mccallm at gmail.com>
>>Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
>>Subject: Re: [BioC] using frma and brainarray cdf on exon arrays
>>Message-ID:
>>	
>><f71eeb981506499f9b6e0c317b4eb53a at CO2PR04MB601.namprd04.prod.outlook.co
>>m>
>>	
>>Content-Type: text/plain; charset="iso-8859-1"
>>
>>Hi Matt,
>>
>>Thanks for the quick reply and the suggestions.  I'll look into making
>>my own pd annotation and frmavecs packages.
>>
>>Ty
>>
>>
>>-----Original Message-----
>>From: Matthew McCall [mailto:mccallm at gmail.com]
>>Sent: Monday, January 13, 2014 3:14 PM
>>To: Ty Thomson
>>Cc: bioconductor at r-project.org
>>Subject: Re: using frma and brainarray cdf on exon arrays
>>
>>Ty,
>>
>>Unfortunately, what you are attempting to do is not currently
>>implemented. The frmavecs packages for the 3' Affy arrays (HGU133a,
>>HGU133plus2, etc) contain implementations for both the Affy and
>>BrainArray CDFs. The issue is with the newer Affy arrays (HuGene 1.0
>>ST, etc.), which should really be read in using the oligo package and
>>corresponding pd annotation packages. This is implemented in frma for
>>the Affy annotation, but currently the BrainArray folks provide CDFs,
>>which can't be readily used. This may be changing fairly soon -- I
>>believe the BrainArray group may start offering oligo compatible
>>annotation packages.
>>Until then, to do what you would like would
>>require: (1) making your own pd annotation package corresponding to the
>>BrainArray alternative CDF, and (2) creating your own frmavecs package
>>for the alternative annotation.
>>
>>Best,
>>Matt
>>
>>
>>On Mon, Jan 13, 2014 at 2:53 PM, Ty Thomson <tthomson at selventa.com>
>>wrote:
>>>Apologies if any of my questions are na?ve, as I don't have a lot of
>>>experience with exon arrays.  I would like to analyze an Affy HuGene
>>>1.0 ST array using the brainArray CDF (because I want to get
>>>expression values on a per gene level), and use fRMA (to correct for
>>>batch effects and enable me to add additional samples in the future
>>>without redoing RMA).  Is this possible?  Here's what I've tried
>>>without much success thus far:
>>>
>>>
>>>
>>>I can skip brainarray and just load the data and run fRMA without error:
>>>
>>>>exonFS <- read.celfiles(filenames=cel.files, verbose=F,
>>>>celfile.path=NULL)
>>>
>>>>tmp.eset <- frma(exonFS, summarize="median_polish")
>>>
>>>
>>>
>>>But when I use ReadAffy and specify the cdf, fRMA generates an error:
>>>
>>>>Affybatch <- ReadAffy(filenames=cel.files, verbose=F,
>>>>celfile.path=NULL,
>>>>cdfname="hugene10sthsentrezg")
>>>
>>>Warning message:
>>>
>>>
>>>
>>>The affy package can process data from the Gene ST 1.x series of
>>>arrays,
>>>
>>>but you should consider using either the oligo or xps packages, which
>>>are specifically
>>>
>>>designed for these arrays.
>>>
>>>
>>>
>>>>tmp.eset <- frma(Affybatch, summarize="median_polish")
>>>
>>>Error in frmaMedPol(object, background, normalize, target, input.vecs,
>>>:
>>>
>>>   hugene10stfrmavecs package must be installed first
>>>
>>>In addition: Warning message:
>>>
>>>In library(package, lib.loc = lib.loc, character.only = TRUE,
>>>logical.return = TRUE,  :
>>>
>>>   there is no package called 'hugene10stfrmavecs'
>>>
>>>
>>>
>>>
>>>
>>>When I try running fRMA while directly passing the frmavecs to the
>>>function I get a different error:
>>>
>>>>data(hugene.1.0.st.v1frmavecs)
>>>
>>>>tmp.eset <- frma(Affybatch, summarize="median_polish",
>>>>input.vecs=hugene.1.0.st.v1frmavecs)
>>>
>>>Warning message:
>>>
>>>In log2(pms) - input.vecs$probeVec :
>>>
>>>   longer object length is not a multiple of shorter object length
>>>
>>>
>>>
>>>
>>>
>>>Thanks in advance for any help,
>>>
>>>
>>>
>>>Ty
>>>
>>>
>>>
>>>
>>>
>>>>sessionInfo()
>>>
>>>R version 3.0.1 (2013-05-16)
>>>
>>>Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>
>>>
>>>
>>>locale:
>>>
>>>[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>>>States.1252    LC_MONETARY=English_United States.1252
>>>
>>>[4] LC_NUMERIC=C                           LC_TIME=English_United
>>>States.1252
>>>
>>>
>>>
>>>attached base packages:
>>>
>>>[1] parallel  stats     graphics  grDevices utils     datasets  methods
>>>base
>>>
>>>
>>>
>>>other attached packages:
>>>
>>>[1] hugene10sthsentrezgcdf_17.1.0  AnnotationDbi_1.22.6
>>>hugene.1.0.st.v1frmavecs_0.0.3 pd.hugene.1.0.st.v1_3.8.0
>>>
>>>  [5] RSQLite_0.11.4                 DBI_0.2-7
>>>frma_1.12.0                    oligo_1.24.2
>>>
>>>  [9] oligoClasses_1.22.0            affy_1.38.1
>>>Biobase_2.20.1                 BiocGenerics_0.6.0
>>>
>>>
>>>
>>>loaded via a namespace (and not attached):
>>>
>>>[1] affxparser_1.32.3     affyio_1.28.0         BiocInstaller_1.10.4
>>>Biostrings_2.28.0     bit_1.1-11            codetools_0.2-8
>>>
>>>  [7] ff_2.2-12             foreach_1.4.1         GenomicRanges_1.12.5
>>>IRanges_1.18.4        iterators_1.0.6       MASS_7.3-29
>>>
>>>[13] preprocessCore_1.22.0 splines_3.0.1         stats4_3.0.1
>>>tools_3.0.1           zlibbioc_1.6.0
>>
>