[BioC] ChIPpeakAnno::getEnrichedGo crashes but I don't know why
Eric Cabot
elcabot at gmail.com
Wed Jan 5 18:29:53 CET 2011
Hi Julie,
Thank you for your response.
Here is the sessionInfo and traceback output and also a few lines of
"my_annotated_regions".
Regards,
Eric Cabot
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChIPpeakAnno_1.6.0 limma_3.6.9
[3] org.Hs.eg.db_2.4.6 GO.db_2.4.5
[5] RSQLite_0.9-4 DBI_0.2-5
[7] AnnotationDbi_1.12.0 BSgenome.Ecoli.NCBI.20080805_1.3.16
[9] BSgenome_1.18.2 GenomicRanges_1.2.2
[11] Biostrings_2.18.2 IRanges_1.8.8
[13] multtest_2.6.0 Biobase_2.10.0
[15] biomaRt_2.6.0
loaded via a namespace (and not attached):
[1] MASS_7.3-9 RCurl_1.5-0 splines_2.12.1 survival_2.36-2
[5] tools_2.12.1 XML_3.2-0
>
my_enrichedGO<-getEnrichedGO(my_annotated_regions,orgAnn="org.Hs.eg.db",maxP=0.01,multiAdj=FALSE,minGOterm=1,feature_id_type="ensembl_gene_id")
Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { :
argument is of length zero
> traceback()
2: addAncestors(this.GO[this.GO[, 3] == "BP", ], "bp")
1: getEnrichedGO(FC2_annotated_regions, orgAnn = "org.Hs.eg.db",
maxP = 0.01, multiAdj = FALSE, minGOterm = 1, feature_id_type =
"ensembl_gene_id")
> as.data.frame(my_annotated_regions[1:15,])
space start end width names peak strand
1 1 241997936 241998205 270 R-10060 ENSE00001749374 R-10060 +
2 1 237109743 237110002 260 R-10082 ENSE00001643382 R-10082 +
3 1 236080267 236080415 149 R-10086 ENSE00001807176 R-10086 +
4 1 233853245 233853514 270 R-10096 ENSE00001776382 R-10096 +
5 1 233727956 233728104 149 R-10097 ENSE00001442190 R-10097 +
6 1 230728554 230728823 270 R-10108 ENSE00001731401 R-10108 +
7 1 229687129 229687277 149 R-10113 ENSE00001439385 R-10113 +
8 1 228943263 228943412 150 R-10121 ENSE00001903546 R-10121 +
9 1 218358885 218359176 292 R-10157 ENSE00001439386 R-10157 +
10 1 212254259 212254408 150 R-10179 ENSE00001624346 R-10179 +
11 1 210086264 210086513 250 R-10184 ENSE00001903225 R-10184 +
12 1 209863549 209863698 150 R-10185 ENSE00001336255 R-10185 +
13 1 207437117 207437264 148 R-10190 ENSE00001742112 R-10190 +
14 1 190352400 190352548 149 R-10246 ENSE00001782518 R-10246 +
15 1 184432607 184432755 149 R-10260 ENSE00001283926 R-10260 +
feature start_position end_position insideFeature
distancetoFeature
1 ENSE00001749374 241995237 241996089 downstream 2699
2 ENSE00001643382 237144639 237145008 upstream -34896
3 ENSE00001807176 236078715 236078821 downstream 1552
4 ENSE00001776382 233807017 233807237 downstream 46228
5 ENSE00001442190 233749750 233750272 upstream -21794
6 ENSE00001731401 230728406 230728586 overlapEnd 148
7 ENSE00001439385 229685652 229685769 downstream 1477
8 ENSE00001903546 228882063 228882416 downstream 61200
9 ENSE00001439386 218303137 218303294 downstream 55748
10 ENSE00001624346 212253973 212254092 downstream 286
11 ENSE00001903225 210111538 210111622 upstream -25274
12 ENSE00001336255 209859550 209859630 downstream 3999
13 ENSE00001742112 207438342 207438381 upstream -1225
14 ENSE00001782518 190331193 190331400 downstream 21207
15 ENSE00001283926 184446520 184446737 upstream -13913
shortestDistance fromOverlappingOrNearest
1 1847 NearestStart
2 34637 NearestStart
3 1446 NearestStart
4 46008 NearestStart
5 21646 NearestStart
6 32 NearestStart
7 1360 NearestStart
8 60847 NearestStart
9 55591 NearestStart
10 167 NearestStart
11 25025 NearestStart
12 3919 NearestStart
13 1078 NearestStart
14 21000 NearestStart
15 13765 NearestStart
Zhu, Lihua (Julie) wrote:
> Hi Eric,
>
> Could you please post the session information with sessionInfo() command?
> Could you please also send a few ensembl IDs in your annotated dataset?
> Thanks!
>
> Best regards,
>
> Julie
>
>
> On 1/4/11 6:51 PM, "Eric Cabot" <elcabot at gmail.com> wrote:
>
>> I am a relatively new Bioconductor user and I am trying to analyze some
>> ChIP-seq results that came from QuEST using the ChIPpeakAnno package.
>>
>> After importing the regions of interest into RangedData objects and doing
>> the following:
>>
>>
> ENSEMBLE_GENES_MART<-useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl">
> )
>> ENSEMBL_ExonPlus_Annotation<-getAnnotation(ENSEMBLE_GENES_MART,
>> featureType="ExonPlusUtr")
>>
>>
>> I had no problem annotating and generating a Venn diagram to show the
>> overlaps between my three sets of peaks. To annotate, I used:
>>
>> annotated_regions=annotatePeakInBatch(myranged,
>> AnnotationData=ENSEMBL_ExonPlus_Annotation)
>>
>>
>> But I cannot seem to get the getEnrichedGo method to work on this (or my
>> other two annotated regions). Here is a typical command line:
>>
>>
>> my_enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db",maxP=0.01
>> ,multiAdj=TRUE,minGOterm=1,
>> multiAdjMethod="BH",feature_id_type="ensembl_gene_id")
>>
>> and here is a typical error message:
>>
>> enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db",maxP=0.01,mu
>> ltiAdj=TRUE,minGOterm=1,feature_id_type="ensembl_gene_id")
>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { :
>> argument is of length zero
>>
>>
>> Which leads me to ask:
>>
>> 1) Is this error message supposed to be meaningful to me-i.e. a user-or is
>> it something that I should be sending to the developer of the package?
>>
>> 2) Is there anything obvious from this that suggests what corrective
>> action I should be taking?
>>
>>
>> Eric Cabot
>> University of Wisconsin
>>
>> _______________________________________________
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>>
>
>
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