error with getBM function of biomaRt package
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T Joshi ▴ 90
@t-joshi-3142
Last seen 9.6 years ago
Hi, I was running the example in getBM and got the following error: getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name","b and"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_at") , mart=mart) Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", "chromosome_name", : could not find function "postForm" Here is the sessionInfo: > sessionInfo() R version 2.7.1 (2008-06-23) ia64-unknown-linux-gnu attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.1 [4] survival_2.34-1 RBGL_1.18.0 annotate_1.18.0 [7] xtable_1.5-4 GO.db_2.2.0 AnnotationDbi_1.2.2 [10] RSQLite_0.6-9 DBI_0.2-4 Biobase_2.0.1 [13] graph_1.18.1 biomaRt_1.14.1 RCurl_0.0.666 loaded via a namespace (and not attached): [1] cluster_1.11.11 tcltk_2.7.1 XML_1.96-0 I also tried with some other data, but it doesn't seem to work anyway. I have attached the output of debug to this mail. Please let me know what's happening here. regards, Josh
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@james-w-macdonald-5106
Last seen 15 hours ago
United States
Hi Josh, The version of RCurl that you have seems to be really old to me. The version used by BioC 2.3 is 0.92-0. You might try biocLite("RCurl"), or better yet, upgrade to R-2.8.0 and BioC 2.3. Best, Jim T Joshi wrote: > Hi, > I was running the example in getBM and got the following error: > > getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name", "band"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_at "), > mart=mart) > Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", > "chromosome_name", : > could not find function "postForm" > > Here is the sessionInfo: >> sessionInfo() > R version 2.7.1 (2008-06-23) > ia64-unknown-linux-gnu > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.1 > [4] survival_2.34-1 RBGL_1.18.0 annotate_1.18.0 > [7] xtable_1.5-4 GO.db_2.2.0 AnnotationDbi_1.2.2 > [10] RSQLite_0.6-9 DBI_0.2-4 Biobase_2.0.1 > [13] graph_1.18.1 biomaRt_1.14.1 RCurl_0.0.666 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 tcltk_2.7.1 XML_1.96-0 > > I also tried with some other data, but it doesn't seem to work anyway. > I have attached the output of debug to this mail. Please let me know > what's happening here. > > regards, > Josh > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
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Hi, Thank you James, Installing RCurl package again solved the problem. Josh On Wed, Dec 3, 2008 at 2:25 PM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Josh, > > The version of RCurl that you have seems to be really old to me. The version > used by BioC 2.3 is 0.92-0. You might try biocLite("RCurl"), or better yet, > upgrade to R-2.8.0 and BioC 2.3. > > Best, > > Jim > > > > T Joshi wrote: >> >> Hi, >> I was running the example in getBM and got the following error: >> >> >> getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name" ,"band"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_a t"), >> mart=mart) >> Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", >> "chromosome_name", : >> could not find function "postForm" >> >> Here is the sessionInfo: >>> >>> sessionInfo() >> >> R version 2.7.1 (2008-06-23) >> ia64-unknown-linux-gnu >> attached base packages: >> [1] splines tools stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.1 >> [4] survival_2.34-1 RBGL_1.18.0 annotate_1.18.0 >> [7] xtable_1.5-4 GO.db_2.2.0 AnnotationDbi_1.2.2 >> [10] RSQLite_0.6-9 DBI_0.2-4 Biobase_2.0.1 >> [13] graph_1.18.1 biomaRt_1.14.1 RCurl_0.0.666 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.11 tcltk_2.7.1 XML_1.96-0 >> >> I also tried with some other data, but it doesn't seem to work anyway. >> I have attached the output of debug to this mail. Please let me know >> what's happening here. >> >> regards, >> Josh >> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Hildebrandt Lab > 8220D MSRB III > 1150 W. Medical Center Drive > Ann Arbor MI 48109-0646 > 734-936-8662 >
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