An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080211/ c32ac70e/attachment.pl

Hi Farrel, Farrel Buchinsky wrote: > Any idea why I get this message > > b <-readGenes("pedformat.txt",gformat="ped") > Error in FUN(X[[2L]], ...) : cannot coerce to vector I don't see that error. However, the pedfile you show below won't work anyway. The first line needs to contain some marker names. This version worked for me (saved as temp.ped): one two three 100 1 0 0 1 1 2 1 2 1 2 100 2 0 0 2 1 2 1 2 1 2 100 3 1 2 1 1 1 2 2 1 1 > readGenes("temp.ped", gformat="ped") Reading 3 markers and 3 subjects from ` temp.ped ' ... generating 'geneSet' object... Successfully read the pedigree file ` temp.ped '. Number of Markers: 3 Number of Subjects: 3 Number of Families: 1 geneSet object ------------------ Number of Markers: 3 Number of Observations: 3 Sample variables: family, pid, father, mother, sex Genetic data: 100.1 100.2 100.3 one 1/2 1/2 1/1 two 1/2 1/2 2/2 three 1/2 1/2 1/1 > sessionInfo() R version 2.6.0 Patched (2007-10-20 r43232) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GeneticsBase_1.2.0 haplo.stats_1.3.1 mvtnorm_0.8-1 xtable_1.5-2 [5] combinat_0.0-6 rcompgen_0.1-17 loaded via a namespace (and not attached): [1] gdata_2.4.0 gplots_2.3.2 gtools_2.4.0 MASS_7.2-37 tools_2.6.0 Best, Jim > > Where pedformat.txt was diretly copied from > http://www.sph.umich.edu/csg/abecasis/GOLD/docs/pedigree.html > 100 1 0 0 1 1 2 1 2 1 2 > 100 2 0 0 2 1 2 1 2 1 2 > 100 3 1 2 1 1 1 2 2 1 1 > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

Farrel Buchinsky wrote: > Any idea why I get this message > > b <-readGenes("pedformat.txt",gformat="ped") > Error in FUN(X[[2L]], ...) : cannot coerce to vector > > Where pedformat.txt was diretly copied from > http://www.sph.umich.edu/csg/abecasis/GOLD/docs/pedigree.html > 100 1 0 0 1 1 2 1 2 1 2 > 100 2 0 0 2 1 2 1 2 1 2 > 100 3 1 2 1 1 1 2 2 1 1 > > Dear Farrel, thank you for your feedback. Can you please include the output of "sessionInfo()" to show versions of R and all attached packages? Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber