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]]
>
> _______________________________________________
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