Hi all, I am trying to use the affy package to analyze GeneChip? Mouse Gene 1.0 ST Array data. What do I need to do to get the CDF information for this chip? I am loading the mogene10st.db package, but that doesnt seem to be correct. Thanks a lot, Peter > library(affy) Lade n?tiges Paket: Biobase Lade n?tiges Paket: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Lade n?tiges Paket: affyio Lade n?tiges Paket: preprocessCore > library(mogene10st.db) Lade n?tiges Paket: AnnotationDbi Lade n?tiges Paket: DBI > myAffy = ReadAffy(filenames=celfiles) > myAffy AffyBatch object size of arrays=1050x1050 features (11 kb) cdf=MoGene-1_0-st-v1 (??? affyids) number of samples=24 Fehler in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain MoGene-1_0-st-v1 Library - package mogene10stv1cdf not installed Data for package affy did not contain mogene10stv1cdf Bioconductor - mogene10stv1cdf not available Zus?tzlich: Warning message: missing cdf environment! in show(AffyBatch) > sessionInfo() R version 2.8.1 (2008-12-22) i486-pc-linux-gnu locale: LC_CTYPE=de_DE at euro;LC_NUMERIC=C;LC_TIME=de_DE at euro;LC_COLLATE=de_DE at euro;LC_MONETARY=C;LC_MESSAGES=de_DE at euro;LC_PAPER=de_DE at euro;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE at euro;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] mogene10st.db_1.0.2 RSQLite_0.6-4 DBI_0.2-4 [4] AnnotationDbi_1.4.3 affy_1.18.2 preprocessCore_1.2.0 [7] affyio_1.8.0 Biobase_2.0.1

On Sun, Mar 1, 2009 at 5:14 AM, Peter Robinson <peter.robinson@t-online.de>wrote: > Hi all, > > I am trying to use the affy package to analyze GeneChip® Mouse Gene 1.0 ST > Array data. What do I need to do to get the CDF information for this chip? > I am loading the > mogene10st.db package, but that doesnt seem to be correct. > Thanks a lot, Peter > > > library(affy) > Lade nötiges Paket: Biobase > Lade nötiges Paket: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Lade nötiges Paket: affyio > Lade nötiges Paket: preprocessCore > > > library(mogene10st.db) > Lade nötiges Paket: AnnotationDbi > Lade nötiges Paket: DBI > > myAffy = ReadAffy(filenames=celfiles) > > > myAffy > AffyBatch object > size of arrays=1050x1050 features (11 kb) > cdf=MoGene-1_0-st-v1 (??? affyids) > number of samples=24 > Fehler in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain MoGene-1_0-st-v1 > Library - package mogene10stv1cdf not installed > Data for package affy did not contain mogene10stv1cdf > Bioconductor - mogene10stv1cdf not available > Zusätzlich: Warning message: > missing cdf environment! in show(AffyBatch) > > Hi, Peter. The affy package will not work with ST arrays. See this page for options: http://bioconductor.org/docs/workflows/oligoarrays/ Sean > > > sessionInfo() > R version 2.8.1 (2008-12-22) > i486-pc-linux-gnu > > locale: > LC_CTYPE=de_DE@euro;LC_NUMERIC=C;LC_TIME=de_DE@euro;LC_COLLATE=de_DE @euro > ;LC_MONETARY=C;LC_MESSAGES=de_DE@euro;LC_PAPER=de_DE@euro > ;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE@euro > ;LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] mogene10st.db_1.0.2 RSQLite_0.6-4 DBI_0.2-4 > [4] AnnotationDbi_1.4.3 affy_1.18.2 preprocessCore_1.2.0 > [7] affyio_1.8.0 Biobase_2.0.1 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi Peter, This chip is supported in Custom CDF version 11, you can google 'custom cdf' for detail. Best, Manhong > Date: Sun, 01 Mar 2009 11:14:50 +0100 > From: Peter Robinson <peter.robinson at="" t-online.de=""> > Subject: [BioC] Cannot find MoGene-1.0 > To: Bioconductor at stat.math.ethz.ch > Message-ID: <49AA601A.90204 at t-online.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi all, > > I am trying to use the affy package to analyze GeneChip? Mouse Gene 1.0 > ST Array data. What do I need to do to get the CDF information for this > chip? I am loading the > mogene10st.db package, but that doesnt seem to be correct. > Thanks a lot, Peter > > > library(affy) > Lade n?tiges Paket: Biobase > Lade n?tiges Paket: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Lade n?tiges Paket: affyio > Lade n?tiges Paket: preprocessCore > > > library(mogene10st.db) > Lade n?tiges Paket: AnnotationDbi > Lade n?tiges Paket: DBI > > myAffy = ReadAffy(filenames=celfiles) > > > myAffy > AffyBatch object > size of arrays=1050x1050 features (11 kb) > cdf=MoGene-1_0-st-v1 (??? affyids) > number of samples=24 > Fehler in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain MoGene-1_0-st-v1 > Library - package mogene10stv1cdf not installed > Data for package affy did not contain mogene10stv1cdf > Bioconductor - mogene10stv1cdf not available > Zus?tzlich: Warning message: > missing cdf environment! in show(AffyBatch) > > > > sessionInfo() > R version 2.8.1 (2008-12-22) > i486-pc-linux-gnu > > locale: > LC_CTYPE=de_DE at euro;LC_NUMERIC=C;LC_TIME=de_DE at euro;LC_COLLATE=de_DE at euro;LC_MONETARY=C;LC_MESSAGES=de_DE at euro;LC_PAPER=de_DE at euro;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE at euro;LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] mogene10st.db_1.0.2 RSQLite_0.6-4 DBI_0.2-4 > [4] AnnotationDbi_1.4.3 affy_1.18.2 preprocessCore_1.2.0 > [7] affyio_1.8.0 Biobase_2.0.1 >