Question: GeneAnswer package Query
0
gravatar for Reema Singh
7.3 years ago by
Reema Singh570
Reema Singh570 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. Regards Reema Singh [[alternative HTML version deleted]]
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ADD COMMENTlink modified 7.3 years ago by Gilbert Feng300 • written 7.3 years ago by Reema Singh570
Answer: GeneAnswer package Query
0
gravatar for Steve Lianoglou
7.3 years ago by
Denali
Steve Lianoglou12k wrote:
Hi Reema, On Sat, Sep 1, 2012 at 11:11 AM, Reema Singh <reema28sep at="" 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
ADD COMMENTlink written 7.3 years ago by Steve Lianoglou12k
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]]
ADD REPLYlink written 7.3 years ago by Sean Davis21k
Answer: GeneAnswer package Query
0
gravatar for Gilbert Feng
7.3 years ago by
Gilbert Feng300
Gilbert Feng300 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 at r-project.org" <bioconductor-request at="" 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 at="" gmail.com=""> >To: bioconductor <bioconductor at="" r-project.org=""> >Subject: [BioC] GeneAnswer package Query >Message-ID: > <caehmz4udwoubclhmzcbecvn4047n9_jhrqdjynaym+0tepagka at="" 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 at="" gmail.com=""> >To: Reema Singh <reema28sep at="" gmail.com=""> >Cc: bioconductor <bioconductor at="" r-project.org=""> >Subject: Re: [BioC] GeneAnswer package Query >Message-ID: > <caha9mcni2wvttveegb2g3=8xq7_fgbvpbb_ojjsoe8gf8zg9gw at="" 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 at="" 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 at="" mail.nih.gov=""> >To: Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> >Cc: bioconductor <bioconductor at="" r-project.org=""> >Subject: Re: [BioC] GeneAnswer package Query >Message-ID: > <caneavbkl2hookmv5v2z5rv1npwfnizolrywokrfjec04kfhs-w at="" mail.gmail.com=""> >Content-Type: text/plain > >On Sat, Sep 1, 2012 at 11:20 AM, Steve Lianoglou < >mailinglist.honeypot at gmail.com> wrote: > >> Hi Reema, >> >> On Sat, Sep 1, 2012 at 11:11 AM, Reema Singh <reema28sep at="" 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]]
ADD COMMENTlink written 7.3 years ago by Gilbert Feng300
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]]
ADD REPLYlink written 7.3 years ago by Reema Singh570
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<mailto:reema28sep@gmail.com>> Date: Sunday, September 2, 2012 1:09 PM To: Bioinformatics Core <g-feng@northwestern.edu<mailto:g-feng@northwestern.edu>> Cc: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto: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<mailto: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<mailto :bioconductor-request@r-project.org="">" <bioconductor-request@r-project.org<mailto: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<mailto:reema28sep@gmail.com>> >To: bioconductor <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> >Subject: [BioC] GeneAnswer package Query >Message-ID: > <caehmz4udwoubclhmzcbecvn4047n9_jhrqdjynaym+0tepagka@mail.gmai l.com<mailto:caehmz4udwoubclhmzcbecvn4047n9_jhrqdjynaym%2b0tepagka@mai="" l.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<mailto:mailingl ist.honeypot@gmail.com="">> >To: Reema Singh <reema28sep@gmail.com<mailto:reema28sep@gmail.com>> >Cc: bioconductor <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> >Subject: Re: [BioC] GeneAnswer package Query >Message-ID: > <caha9mcni2wvttveegb2g3=8xq7_fgbvpbb_ojjsoe8gf8zg9gw@mail.gmai l.com<mailto: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<mailto: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<http: cbio.mskcc="" .org="" %7elianos="" contact=""> > > > >------------------------------ > >Message: 10 >Date: Sat, 1 Sep 2012 11:23:46 -0400 >From: Sean Davis <sdavis2@mail.nih.gov<mailto:sdavis2@mail.nih.gov>> >To: Steve Lianoglou <mailinglist.honeypot@gmail.com<mailto:mailinglis t.honeypot@gmail.com="">> >Cc: bioconductor <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> >Subject: Re: [BioC] GeneAnswer package Query >Message-ID: > <caneavbkl2hookmv5v2z5rv1npwfnizolrywokrfjec04kfhs-w@mail.gmai l.com<mailto:caneavbkl2hookmv5v2z5rv1npwfnizolrywokrfjec04kfhs-w@mail.="" gmail.com="">> >Content-Type: text/plain > >On Sat, Sep 1, 2012 at 11:20 AM, Steve Lianoglou < >mailinglist.honeypot@gmail.com<mailto:mailinglist.honeypot@gmail.com> > wrote: > >> Hi Reema, >> >> On Sat, Sep 1, 2012 at 11:11 AM, Reema Singh <reema28sep@gmail.com<mailto: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<mailto: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]]
ADD REPLYlink written 7.3 years ago by Gilbert Feng300
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]]
ADD REPLYlink written 7.3 years ago by Reema Singh570
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]]
ADD REPLYlink written 7.3 years ago by Reema Singh570
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