fRMA for Gene ST arrays
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maria ▴ 10
@maria-6339
Last seen 7.2 years ago
> > > Kamila, > > You can preprocess Gene ST arrays using the latest version of frma -- > just load the data using the oligo package. And you can obtain GNUSE > values using the GNUSE function on the preprocessed data object. > > A barcode implementation for the Gene ST arrays is not currently > available, but it is in the works -- hopefully it will be ready before > the fall BioC release. > > Best, > Matt > > On Wed, Apr 3, 2013 at 8:41 AM, Naxerova, Kamila > <naxerova at="" ...=""> wrote: > > Dear list, > > > > to preprocess Affymetrix whole transcript arrays, use of oligo and xps is recommended over the affy > package. I am interested in using the GNUSE algorithm to assign quality scores to some arrays, and would > also like to try out the barcode function in the frma package. I am now wondering... is frma compatible with > whole transcript arrays? > > > > Thanks a lot. > > Kamila > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at ... > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > Hi, First, I apologize if I posted this message at the wrong place. I tried to run barcode for the hugene.1.0.st.v1 and got an output for only 4000 probes. The problem seems that when barcode maps the probe names from "hugene.1.0.st.v1frmavecs" to my data the overlap is only of 4000 although tau and mu contains about 37000 items. I wonder if I did a mistake in my coding (I'm new in microarray analysis) or if this is really what happens. (see script below). I also tried to edit the code of barcode to add a new platform and I assigned the vector hugene.1.0.st.v1frmavecs to the pkg. (pkg <- "hugene.1.0.st.v1frmavecs") but it does not help. Thank you in advance for your help Maria library("oligo") library(pd.hugene.1.0.st.v1) celFiles = list.celfiles() affyRaw= read.celfiles(celFiles) library("hugene.1.0.st.v1frmavecs") data("hugene.1.0.st.v1frmavecs") data("hugene.1.0.st.v1barcodevecs") library("frma") eset=frma(affyRaw,input.vecs=hugene.1.0.st.v1frmavecs, summarize="median_polish" ) b=barcode(exprs(eset),platform=NULL,mu=hugene.1.0.st.v1barcodevecs$mu, tau=hugene.1.0.st.v1barcodevecs$tau, output="p-value") R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32/i386 (32-bit) attached base packages: [1] stats graphics utils methods base other attached packages: [1] frma_1.10.0 hugene.1.0.st.v1frmavecs_1.0.0 [3] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.4 [5] DBI_0.2-7 oligo_1.22.0 [7] Biobase_2.18.0 oligoClasses_1.20.0 [9] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affxparser_1.30.2 affy_1.36.1 affyio_1.26.0 [4] BiocInstaller_1.8.3 Biostrings_2.26.3 bit_1.1-11 [7] codetools_0.2-8 ff_2.2-12 foreach_1.4.1 [10] GenomicRanges_1.10.7 grDevices_2.15.2 IRanges_1.16.6 [13] iterators_1.0.6 MASS_7.3-23 parallel_2.15.2 [16] preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 [19] tools_2.15.2 zlibbioc_1.4.0
Microarray probe oligo frma Microarray probe oligo frma • 1.5k views
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Entering edit mode
@matthew-mccall-4459
Last seen 2.4 years ago
United States
Maria, It looks like you version of frma is quite old (the current release version is 1.14.0). I'd start by updating the relevant packages. What are the dimensions of the preprocessed expression values: dim(exprs(eset)) And the dimensions of the barcode values: dim(b) Best, Matt On Thu, Jan 16, 2014 at 10:29 AM, maria <maria.pacheco at="" uni.lu=""> wrote: >> >> >> Kamila, >> >> You can preprocess Gene ST arrays using the latest version of frma -- >> just load the data using the oligo package. And you can obtain GNUSE >> values using the GNUSE function on the preprocessed data object. >> >> A barcode implementation for the Gene ST arrays is not currently >> available, but it is in the works -- hopefully it will be ready before >> the fall BioC release. >> >> Best, >> Matt >> >> On Wed, Apr 3, 2013 at 8:41 AM, Naxerova, Kamila >> <naxerova at="" ...=""> wrote: >> > Dear list, >> > >> > to preprocess Affymetrix whole transcript arrays, use of oligo and xps > is recommended over the affy >> package. I am interested in using the GNUSE algorithm to assign quality > scores to some arrays, and would >> also like to try out the barcode function in the frma package. I am now > wondering... is frma compatible with >> whole transcript arrays? >> > >> > Thanks a lot. >> > Kamila >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at ... >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > Hi, > First, I apologize if I posted this message at the wrong place. I tried to > run barcode for the hugene.1.0.st.v1 and got an output for only 4000 probes. > The problem seems that when barcode maps the probe names from > "hugene.1.0.st.v1frmavecs" to my data the overlap is only of 4000 although > tau and mu contains about 37000 items. I wonder if I did a mistake in my > coding (I'm new in microarray analysis) or if this is really what happens. > (see script below). I also tried to edit the code of barcode to add a new > platform and I assigned the vector hugene.1.0.st.v1frmavecs to the pkg. > (pkg <- "hugene.1.0.st.v1frmavecs") but it does not help. > Thank you in advance for your help > > Maria > > > > > > > library("oligo") > library(pd.hugene.1.0.st.v1) > > celFiles = list.celfiles() > > affyRaw= read.celfiles(celFiles) > > library("hugene.1.0.st.v1frmavecs") > data("hugene.1.0.st.v1frmavecs") > data("hugene.1.0.st.v1barcodevecs") > > > library("frma") > > eset=frma(affyRaw,input.vecs=hugene.1.0.st.v1frmavecs, > summarize="median_polish" ) > > b=barcode(exprs(eset),platform=NULL,mu=hugene.1.0.st.v1barcodevecs$mu, > tau=hugene.1.0.st.v1barcodevecs$tau, output="p-value") > > > > > R version 2.15.2 (2012-10-26) > Platform: i386-w64-mingw32/i386 (32-bit) > > > attached base packages: > [1] stats graphics utils methods base > > other attached packages: > [1] frma_1.10.0 hugene.1.0.st.v1frmavecs_1.0.0 > [3] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.4 > [5] DBI_0.2-7 oligo_1.22.0 > [7] Biobase_2.18.0 oligoClasses_1.20.0 > [9] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.30.2 affy_1.36.1 affyio_1.26.0 > [4] BiocInstaller_1.8.3 Biostrings_2.26.3 bit_1.1-11 > [7] codetools_0.2-8 ff_2.2-12 foreach_1.4.1 > [10] GenomicRanges_1.10.7 grDevices_2.15.2 IRanges_1.16.6 > [13] iterators_1.0.6 MASS_7.3-23 parallel_2.15.2 > [16] preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 > [19] tools_2.15.2 zlibbioc_1.4.0 > > _______________________________________________ > 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 -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880