Sorry i forgot to add sessionInfo in the last mail. Here it is:- > 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 On Mon, Sep 3, 2012 at 10:06 PM, Reema Singh <reema28sep@gmail.com> wrote: > Hello Sir > > This is the output:- > > > dim(getEnrichmentInfo(xx)) > [1] 1 7 > > getEnrichmentInfo(xx) > genes in Category percent in the observed List > protein repair 2 0.06896552 > percent in the genome fold of overrepresents odds ratio > protein repair 0.0002713336 254.1724 544.8519 > p value fdr p value > protein repair 2.236468e-05 0.02030713 > > I have also tried it on a significant (p = 0.0001) down-regulated dataset. > Again get the same error. Here the complete information. > > > head(down) > GeneID foldChange pValue > 100 100 -1.1433261 2.756173e-06 > 10046 10046 -1.2166369 1.671788e-05 > 10135 10135 -1.5519142 3.743193e-06 > 10148 10148 -1.2925089 2.542466e-05 > 10318 10318 -0.5372158 4.012577e-06 > 10512 10512 -0.6394524 1.449433e-05 > > > head(down1.m) > GeneID Stim1 Unstim1 Stim4 Unstim4 Stim4 > Unstim4 > 1 100 3.12750521 2.04147745 3.15678621 2.0224653 2.99997610 > 2.0694252 > 2 10046 1.11009538 -0.01199315 0.65581813 -0.1959238 1.09672062 > -0.3753898 > 3 10135 2.24844320 0.72590576 1.83288587 0.8304263 2.32545893 > 0.6931020 > 4 10148 1.54497833 0.40287259 2.23675264 0.6894496 1.97981608 > 0.9060486 > 5 10318 2.64639957 2.20436381 2.65294262 2.1945730 2.66523991 > 2.0821377 > 6 10512 0.01460591 -0.61158221 0.03587951 -0.4240292 -0.03954363 > -0.6110579 > Stim4 Unstim4 > 1 3.0030792 1.5806744 > 2 0.8126726 -0.6079340 > 3 2.2488694 0.1985666 > 4 1.8028223 0.3959628 > 5 2.6880915 2.0227360 > 6 0.1966093 -0.7035892 > > > x <- geneAnswersBuilder(down, 'org.Hs.eg.db', categoryType='GO.BP', > testType='hyperG', pvalueT=0.1, FDR.correction=TRUE, > geneExpressionProfile=down1.m) > [1] "geneInput has built in ..." > Loading required package: org.Hs.eg.db > > Loading required package: GO.db > [1] "annLib and categoryType have built in ..." > [1] "genesInCategory has built in ..." > [1] "Enrichment test is only performed based on annotated genes" > [1] "testType, pvalueT and enrichmentInfo have built in ..." > [1] "geneExpressionProfile has been built in ..." > [1] "GeneAnswers instance has been successfully created!" > > > > class(x) > [1] "GeneAnswers" > attr(,"package") > [1] "GeneAnswers" > > > xx <- geneAnswersReadable(x) > [1] "Mapping geneInput ..." > [1] "Mapping genesInCategory ..." > [1] "Mapping enrichmentInfo rownames ..." > [1] "Mapping geneExprProfile rownames ..." > > > > class(xx) > [1] "GeneAnswers" > attr(,"package") > [1] "GeneAnswers" > > > geneAnswersConceptNet(xx, colorValueColumn='foldChange', > centroidSize='pvalue', output='interactive') > Error in `*tmp*`[[4]] : subscript out of bounds > > > dim(getEnrichmentInfo(xx)) > [1] 1308 7 > > Regards > Reema Singh > > > > > > On Mon, Sep 3, 2012 at 12:46 AM, Gang Feng <g-feng@northwestern.edu>wrote: > >> Can you run dim(getEnrichmentInfo(xx)) ? Because there is a warning >> here, "Some specified categories might not be statistical significant! Only >> show significant categories.". So if there is none significant pathway >> based on geneAnswersBuilder, you can't get the network. >> >> Gilbert >> >> From: Reema Singh <reema28sep@gmail.com> >> Date: Sunday, September 2, 2012 1:09 PM >> To: Bioinformatics Core <g-feng@northwestern.edu> >> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> >> >> Subject: Re: [BioC] GeneAnswer package Query >> >> 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 <g-feng@northwestern.edu>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" >>> <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 <reema28sep@gmail.com> >>> >To: bioconductor <bioconductor@r-project.org> >>> >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 <mailinglist.honeypot@gmail.com> >>> >To: Reema Singh <reema28sep@gmail.com> >>> >Cc: bioconductor <bioconductor@r-project.org> >>> >Subject: Re: [BioC] GeneAnswer package Query >>> >Message-ID: >>> > <caha9mcni2wvttveegb2g3=>>> 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 <reema28sep@gmail.com> >>> 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 <sdavis2@mail.nih.gov> >>> >To: Steve Lianoglou <mailinglist.honeypot@gmail.com> >>> >Cc: bioconductor <bioconductor@r-project.org> >>> >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 <reema28sep@gmail.com> >>> >>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]]