Hi there, I am getting this error on R console. The format of the input files, Micro_array_dataset.txt and Gene_set.gmt is shown below: Micro_array_dataset.txt sample shown below, it's a tab delimited file: Gene TCGA_AB_2803 TCGA_AB_2805 TCGA_AB_2806 TCGA_AB_2807 TCGA_AB_2808 TCGA_AB_2810 TSPAN6 0.87040619 0 0 1.49516441 0.145067698 0 TNMD 0.14858841 0.037147103 0 0 0 0 DPM1 45.07516892 63.28462838 64.9535473 41.44256757 46.61233108 42.66807432 SCYL3 12.62339374 22.15584843 25.60428336 13.98088962 17.0583196 4.036902801 Gene_set.gmt is a Gene Matrix Transposed file format required for GSEA analysis, sample shown below: chr5q23 na PTMAP2 FTMT PRR16 MGC32805 chr16q24 na LOC642452 SNORD68 RPL13 TRAPPC2L chr8q24 na LYPD2 KIFC2 EIF2C2 ADCY8 chr13q11 na LOC645626 ZMYM2 FGF9 XPO4 chr7p21 na DNAH11 LOC221814 MYL7 CRS Any kind of help to get rid of the error shown below will be really appreciated. Thanks, Jung -- output of sessionInfo(): > Micro_array_data <- readExpData(file = "Micro_array_dataset.txt") > Gene_set <- readList("Gene_set.gmt") > Reference_condition <- c(1,3,5) > Target_condition <- c(2,4,6) > A1_compare_un <- gage(Micro_array_data, Gene_set, ref = Reference_condition, samp = Target_condition) Error in saaPrep(exprs, ref = ref, samp = samp, same.dir = same.dir, compare = compare, : exprs needs to be a numeric matrix or vector > # Essential_member_genes <- essGene(Gene_set, Micro_array_data,ref = NULL) > # Non_redundant_significant_gene_set_list <- esset.grp() > -- Sent via the guest posting facility at bioconductor.org.

On 01/25/2012 10:56 AM, Jung [guest] wrote: > > Hi there, > I am getting this error on R console. The format of the input files, Micro_array_dataset.txt and Gene_set.gmt is shown below: > Micro_array_dataset.txt sample shown below, it's a tab delimited file: > Gene TCGA_AB_2803 TCGA_AB_2805 TCGA_AB_2806 TCGA_AB_2807 TCGA_AB_2808 TCGA_AB_2810 > TSPAN6 0.87040619 0 0 1.49516441 0.145067698 0 > TNMD 0.14858841 0.037147103 0 0 0 0 > DPM1 45.07516892 63.28462838 64.9535473 41.44256757 46.61233108 42.66807432 > SCYL3 12.62339374 22.15584843 25.60428336 13.98088962 17.0583196 4.036902801 > > Gene_set.gmt is a Gene Matrix Transposed file format required for GSEA analysis, sample shown below: > chr5q23 na PTMAP2 FTMT PRR16 MGC32805 > chr16q24 na LOC642452 SNORD68 RPL13 TRAPPC2L > chr8q24 na LYPD2 KIFC2 EIF2C2 ADCY8 > chr13q11 na LOC645626 ZMYM2 FGF9 XPO4 > chr7p21 na DNAH11 LOC221814 MYL7 CRS > > > Any kind of help to get rid of the error shown below will be really appreciated. Hi Jung -- see the help pages for gage (?gage) to find out what 'expr' is supposed to be. See the help page for readExpData (?readExpData; also ?read.delim) and check class(Micro_array_data). Are there any problems? Martin > Thanks, > > Jung > > > > -- output of sessionInfo(): > >> Micro_array_data<- readExpData(file = "Micro_array_dataset.txt") >> Gene_set<- readList("Gene_set.gmt") >> Reference_condition<- c(1,3,5) >> Target_condition<- c(2,4,6) >> A1_compare_un<- gage(Micro_array_data, Gene_set, ref = Reference_condition, samp = Target_condition) > Error in saaPrep(exprs, ref = ref, samp = samp, same.dir = same.dir, compare = compare, : > exprs needs to be a numeric matrix or vector >> # Essential_member_genes<- essGene(Gene_set, Micro_array_data,ref = NULL) >> # Non_redundant_significant_gene_set_list<- esset.grp() >> > > -- > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793