Thankyou so much for the reply. When i tried GeneAnswer with the standarad dataset(example dataset given in the GeneAnswer package) , geneAnswersConceptNet is wotking . But when i use my own data, i got error. here's the complete information. > head(UpPvalue) GeneID foldChange pValue 100129502 100129502 0.3400368 0.0003138338 11041 11041 0.3721243 0.0059766012 168544 168544 0.1848346 0.0082261978 1891 1891 0.1702410 0.0400237055 2242 2242 0.5759854 0.0030583008 22921 22921 0.3572599 0.0163114750 > class(UpPvalue) [1] "data.frame" > mode(UpPvalue) [1] "list" > head(up.m) GeneID Stim1 Unstim1 Stim2 Unstim2 Stim3 1 100129502 -0.112711749 0.27118938 -0.059303044 0.269980812 -0.10985210 2 11041 0.229691563 0.60086507 0.358272967 0.839294988 0.39096888 3 168544 -0.177046627 0.04544861 -0.225278472 0.003436854 -0.04600091 4 1891 1.568946410 1.76194658 1.718906028 1.624777089 1.54661663 5 2242 -0.010019402 0.37031039 -0.062937599 0.532681263 0.05322532 6 22921 0.005099843 0.30712912 -0.008421601 0.174318781 0.10757702 Unstim3 Stim4 Unstim4 1 0.26675219 -0.1924595 0.07789838 2 0.56386919 0.5212347 0.98463626 3 -0.03394248 -0.1925421 0.08352727 4 1.73230233 1.4489762 1.84538314 5 1.01401566 -0.0878877 0.27931473 6 0.78369883 0.1848340 0.45298225 > class(up.m) [1] "data.frame" > mode(up.m) [1] "list" x <- geneAnswersBuilder(UpPvalue, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.1, FDR.correction=TRUE, geneExpressionProfile=up.m) > class(x) [1] "GeneAnswers" attr(,"package") [1] "GeneAnswers" > xx <- geneAnswersReadable(x) > class(xx) [1] "GeneAnswers" attr(,"package") [1] "GeneAnswers" > geneAnswersConceptNet(xx, colorValueColumn='foldChange', centroidSize='pvalue', output='interactive') [1] "Some specified categories might not be statistical significant! Only show significant categories." Error in `*tmp*`[[4]] : subscript out of bounds And the SessionInfo() > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GO.db_2.7.1 org.Hs.eg.db_2.7.1 GeneAnswers_1.12.2 [4] Heatplus_2.2.0 rgl_0.92.880 XML_3.9-4 [7] annotate_1.34.0 RCurl_1.91-1 igraph0_0.5.5-2 [10] clusterProfiler_1.4.0 AnnotationDbi_1.18.1 RSQLite_0.11.1 [13] DBI_0.2-5 MADAM_1.1 impute_1.30.0 [16] gplots_2.11.0 MASS_7.3-19 KernSmooth_2.23-7 [19] caTools_1.13 bitops_1.0-4.1 gdata_2.11.0 [22] gtools_2.7.0 GeneMeta_1.28.0 genefilter_1.38.0 [25] RColorBrewer_1.0-5 RankProd_2.28.0 qvalue_1.30.0 [28] limma_3.12.0 GEOquery_2.23.5 Biobase_2.16.0 [31] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 DO.db_2.4 [5] DOSE_1.2.1 ggplot2_0.9.1 graph_1.34.0 igraph_0.6-2 [9] IRanges_1.14.4 KEGG.db_2.7.1 labeling_0.1 memoise_0.1 [13] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RBGL_1.32.1 [17] reshape2_1.2.1 Rgraphviz_1.34.2 scales_0.2.1 splines_2.15.0 [21] stats4_2.15.0 stringr_0.6 survival_2.36-14 tcltk_2.15.0 [25] tools_2.15.0 xtable_1.7-0 > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GO.db_2.7.1 org.Hs.eg.db_2.7.1 GeneAnswers_1.12.2 [4] Heatplus_2.2.0 rgl_0.92.880 XML_3.9-4 [7] annotate_1.34.0 RCurl_1.91-1 igraph0_0.5.5-2 [10] clusterProfiler_1.4.0 AnnotationDbi_1.18.1 RSQLite_0.11.1 [13] DBI_0.2-5 MADAM_1.1 impute_1.30.0 [16] gplots_2.11.0 MASS_7.3-19 KernSmooth_2.23-7 [19] caTools_1.13 bitops_1.0-4.1 gdata_2.11.0 [22] gtools_2.7.0 GeneMeta_1.28.0 genefilter_1.38.0 [25] RColorBrewer_1.0-5 RankProd_2.28.0 qvalue_1.30.0 [28] limma_3.12.0 GEOquery_2.23.5 Biobase_2.16.0 [31] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 DO.db_2.4 [5] DOSE_1.2.1 ggplot2_0.9.1 graph_1.34.0 igraph_0.6-2 [9] IRanges_1.14.4 KEGG.db_2.7.1 labeling_0.1 memoise_0.1 [13] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RBGL_1.32.1 [17] reshape2_1.2.1 Rgraphviz_1.34.2 scales_0.2.1 splines_2.15.0 [21] stats4_2.15.0 stringr_0.6 survival_2.36-14 tcltk_2.15.0 [25] tools_2.15.0 xtable_1.7-0 Regards Reema Singh On Sun, Sep 2, 2012 at 10:55 PM, Gang Feng wrote: > Hi, Reema > > Please give us more info, like Steve and Sean stated in their previous > responses. > > Basically, for geneAnswersConceptNet(), xx should be an instance of > GeneAnswers. So you can run > > class(xx) > > If the output is not like this, > > [1] "GeneAnswers" > attr(,"package") > [1] "GeneAnswers" > > > You need geneAnswersBuilder() to build a GeneAnswers instance at first. > > There is one thing that you might need to know. Because of a large update > (especially index change) of igraph, which is one of GeneAnswers dependent > packages, the current version, 0.6.x does NOT work with GeneAnswers. The > developer of igraph provides a temp solution, igraph0, an old version of > igraph. So each time, when you launch R and GeneAnswers WITHOUT starting > the latest igraph, the current GeneAnswers is fine. But once you launch > the new igraph, all of network related functions won't work. We are > working on this issue right now and hope that the new version GeneAnswers > in OCT will work with the new igraph and Reactome.db . > > Thanks > > Gilbert > > > BTW, does anyone know how I can directly reply the original thread in > daily digest? I searched online, but didn't get any clue. Thanks a lot! > > On 9/2/12 5:00 AM, "bioconductor-request@r-project.org" > wrote: > > > 8. GeneAnswer package Query (Reema Singh) > > 9. Re: GeneAnswer package Query (Steve Lianoglou) > > 10. Re: GeneAnswer package Query (Sean Davis) > > > > > >------------------------------ > > > >Message: 8 > >Date: Sat, 1 Sep 2012 20:41:46 +0530 > >From: Reema Singh > >To: bioconductor > >Subject: [BioC] GeneAnswer package Query > >Message-ID: > > < > CAEHmZ4uDWoubcLHMzCbecvn4047N9_JhRqDjYNAYM+0TEpAgkA@mail.gmail.com> > >Content-Type: text/plain > > > >Dear all > > > >I am getting following error, when try to get network graph using > >GeneAnswer package > > > >> geneAnswersConceptNet(xx, colorValueColumn='foldChange', > >centroidSize='pvalue', output='interactive') > > > > Error in `*tmp*`[[4]] : subscript out of bounds > > > >Any suggestion would be a great help. > > > >Regards > >Reema Singh > > > > [[alternative HTML version deleted]] > > > > > > > >------------------------------ > > > >Message: 9 > >Date: Sat, 1 Sep 2012 11:20:48 -0400 > >From: Steve Lianoglou > >To: Reema Singh > >Cc: bioconductor > >Subject: Re: [BioC] GeneAnswer package Query > >Message-ID: > > 8xQ7_fgBVpbB_OjJSoE8Gf8zg9Gw@mail.gmail.com> > >Content-Type: text/plain; charset=ISO-8859-1 > > > >Hi Reema, > > > >On Sat, Sep 1, 2012 at 11:11 AM, Reema Singh > wrote: > >> Dear all > >> > >> I am getting following error, when try to get network graph using > >> GeneAnswer package > >> > >>> geneAnswersConceptNet(xx, colorValueColumn='foldChange', > >> centroidSize='pvalue', output='interactive') > >> > >> Error in `*tmp*`[[4]] : subscript out of bounds > >> > >> Any suggestion would be a great help. > > > >You'd need to give us some reproducible example to help us to help you > >best ... for instance, what's in `xx`? Is it a matrix? data.frame? > >list? something else? > > > >You might be able to start to help yourself by calling `traceback()` > >after the error is fired to see where inside the > >`geneAnswersConceptNet` the error occurs -- this will also require you > >to start looking at the code of the `geneAnswersConceptNet` function > >to see why you are missing some expected index (which is always a good > >idea to do when you get such problems, anyway). > > > >HTH, > >-steve > > > >-- > >Steve Lianoglou > >Graduate Student: Computational Systems Biology > > | Memorial Sloan-Kettering Cancer Center > > | Weill Medical College of Cornell University > >Contact Info: http://cbio.mskcc.org/~lianos/contact > > > > > > > >------------------------------ > > > >Message: 10 > >Date: Sat, 1 Sep 2012 11:23:46 -0400 > >From: Sean Davis > >To: Steve Lianoglou > >Cc: bioconductor > >Subject: Re: [BioC] GeneAnswer package Query > >Message-ID: > > < > CANeAVBkL2hOoKmv5V2z5rV1NpWfniZOLryWoKRfJeC04kFhS-w@mail.gmail.com> > >Content-Type: text/plain > > > >On Sat, Sep 1, 2012 at 11:20 AM, Steve Lianoglou < > >mailinglist.honeypot@gmail.com> wrote: > > > >> Hi Reema, > >> > >> On Sat, Sep 1, 2012 at 11:11 AM, Reema Singh > >>wrote: > >> > Dear all > >> > > >> > I am getting following error, when try to get network graph using > >> > GeneAnswer package > >> > > >> >> geneAnswersConceptNet(xx, colorValueColumn='foldChange', > >> > centroidSize='pvalue', output='interactive') > >> > > >> > Error in `*tmp*`[[4]] : subscript out of bounds > >> > > >> > Any suggestion would be a great help. > >> > >> You'd need to give us some reproducible example to help us to help you > >> best ... for instance, what's in `xx`? Is it a matrix? data.frame? > >> list? something else? > >> > >> You might be able to start to help yourself by calling `traceback()` > >> after the error is fired to see where inside the > >> `geneAnswersConceptNet` the error occurs -- this will also require you > >> to start looking at the code of the `geneAnswersConceptNet` function > >> to see why you are missing some expected index (which is always a good > >> idea to do when you get such problems, anyway). > >> > >> > >And don't forget to include sessionInfo(). > > > >Sean > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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]]