Thanks a lot for the help, I will see the vignette and try to analyze my data with these packages. Claudia On Sun, Nov 3, 2013 at 11:26 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > with bioconductor these arrays can be processed with oligo (please see the > vignette) and annotation comes from pd.* packages > > http://www.bioconductor.org/packages/release/bioc/html/oligo.html > > > http://www.bioconductor.org/packages/release/data/annotation/html/pd .hugene.1.0.st.v1.html > > you may also consider xps > > http://www.bioconductor.org/packages/release/bioc/html/xps.html > > > On Sun, Nov 3, 2013 at 4:15 PM, Claudia [guest] <guest@bioconductor.org>wrote: > >> >> Hello, >> >> I'm trying to analyze some array data with Bioconductor and I receive the >> following errore when I try to filter with GeneFilter: Error: getAnnMap: >> package hugene10stv1 not available. >> >> This is the script I'm currently using: >> setwd("C:/raw") >> library(affy) >> library("genefilter") >> mydata <- ReadAffy() >> pData(mydata)<-read.table("phenodata.txt", header=T, >> row.names=1, sep="\t") >> eset <- rma(mydata) >> esetf<-nsFilter(eset) >> >> Annotation is hugene10stv1. I have already installed hugene10stv1cdf and >> hugene10stv1probe packages but I receive the same error every time I try to >> filter my set. >> >> Any help would be very much appreciated. >> >> Thanks a lot >> Claudia >> >> -- output of sessionInfo(): >> >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: i386-w64-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 >> [3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C >> [5] LC_TIME=Italian_Italy.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] hugene10stv1cdf_2.13.0 AnnotationDbi_1.24.0 genefilter_1.44.0 >> [4] affy_1.40.0 Biobase_2.22.0 BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.30.0 annotate_1.40.0 BiocInstaller_1.12.0 >> [4] DBI_0.2-7 IRanges_1.20.4 preprocessCore_1.24.0 >> [7] RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 >> [10] survival_2.37-4 tools_3.0.2 XML_3.98-1.1 >> [13] xtable_1.7-1 zlibbioc_1.8.0 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]