Normalizing Affy Almac Xcel Array Data from CEL files
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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.
Annotation affy oligo ffpe Annotation affy oligo ffpe • 2.3k views
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@james-w-macdonald-5106
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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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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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@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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi Wei, Yes, it is a PM-only array. Rather than using simpleaffy, which is really designed for arrays with PM and MM probes, you might consider using arrayQualityMetrics. The arrayQualityMetrics package uses simpleaffy as well, but will only run those quality measures that pertain to PM-only arrays. Best, Jim On Thursday, January 09, 2014 12:35:48 PM, Dr Wei Chen wrote: > 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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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cstrato ★ 3.9k
@cstrato-908
Last seen 6.2 years ago
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Dear Wei, In principle you could also use package 'xps' for analyzing Xcel Arrays. For xps you can create the necessary 'scheme' file as follows: library(xps) libdir <- "/Volumes/GigaDrive/Affy/libraryfiles" anndir <- "/Volumes/GigaDrive/Affy/Annotation" scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes" # scheme file for Almac Xcel: scheme.xcel.na33 <- import.expr.scheme("xcel", filedir = file.path(scmdir, "na33"), schemefile = file.path(libdir, "Xcel.CDF"), probefile = file.path(libdir, "Xcel.probe.tab"), annotfile = file.path(anndir, "na33", "Xcel.na33.annot.csv")) Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ On 1/7/14 8:03 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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