[BioC] Question: GSVA error
Robert Castelo
robert.castelo at upf.edu
Thu Feb 7 14:46:55 CET 2013
hi,
On 02/07/2013 12:55 PM, chuanbao wrote:
>
>
> Thanks, Robert.
> Comments below as well.
>
>
>
>
> At 2013-02-07 18:27:38,"Robert Castelo" <robert.castelo at upf.edu> wrote:
>>hi Chuanbao,
>>
>>comments below,
>>
>>On 02/07/2013 03:06 AM, chuanbao wrote:
>>> Thanks, Robert. I'm trying to reply the email directly instead of using
>>> the Guest Posting.
>>>
>>> the same error also came up if I used the example data. So I think the
>>> error has nothing to do with the data. Here is the result of the 3
>>> commands if I use my own data.
>>
>>this is strange, because the package builds correctly in the BioC
>>servers for linux, windows and mac, which includes running the
>>vignettes. could you write to me here the code snippet from the vignette
>>that does not run in your system?
>>
>
> Sorry, I don't exactly know the problem. The code snippet? the error only come up if I use the command GSVA in the end. Nothing error messages before that.
in general with this and any other package that prompts an error it is
useful to post in the message piece of code that allows the package
maintainer (in this case, me) to reproduce the error in the maintainer's
computer. you can find this and other useful guidelines in the
bioconductor posting guide at
http://www.bioconductor.org/help/mailing-list/posting-guide
your description of the problem as
"the error only come up if I use the command GSVA in the end. Nothing
error messages before that."
does not allow me to find out what can possibly be going wrong. i need
from you the lines of R that you put in your system and give the error.
however, the output of your sessionInfo() below has given me some clue,
so before you paste any code now, you have to do some step beforehand,
please keep reading..
>>> > dim(expr)
>>> [1] 19416 47
>>> > expr[1:5, 1:5]
>>> X11 X124 X126 X168 X172
>>> BCL2L13 -0.2728815 -0.3151436 0.2537942 -0.04622459 -0.1697597
>>> SFRS13B 1.4056368 0.1155653 -0.2734718 -1.69556520 -0.3463836
>>> HCP5 -0.7666955 -0.2999439 -0.2891264 1.39690780 0.2029056
>>> FAM104B 0.6052895 0.2365847 -0.3497281 -0.15993309 -0.1223259
>>> UBE2T -0.3321409 -0.0476532 -0.1204028 -1.36906810 0.7174168
>>>
>>> > genesets
>>> [[1]]
>>> [1] GRHL1 GPAM PAPSS2 BTG1 SLC46A1 SPIRE1 LYRM4 HEPH CHRDL1
>>> [10] ADORA2B ELOVL2 FGFR3 TMEM51
>>> 27 Levels: ADORA2B AGPAT4 APP ASNS ATP1A1 BCAT1 BTG1 CHRDL1 CORO1C ...
>>> TMEM51
>>>
>>> [[2]]
>>> [1] CYP7B1 ATP1A1 FRMD5 ASNS SEMA3E LPGAT1 RAN AGPAT4 GOT2 BCAT1
>>> [11] CORO1C PAK3 GPR85 APP
>>> 27 Levels: ADORA2B AGPAT4 APP ASNS ATP1A1 BCAT1 BTG1 CHRDL1 CORO1C ...
>>> TMEM51
>>
>>i see that the gene symbols in the genesets are stored as factors, could
>>you translate them into character strings? i.e.
>>
>>genesets <- lapply(genesets, as.character)
>>
>>and try again?
>
> I tried, same problem~~
>>
>>
>>a further fundamental piece of information i was already requesting
>>below, please can you paste the output of
>>
>>sessionInfo()
>>
>>??
>>
>
>> sessionInfo()
> R version 2.13.2 (2011-09-30)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] GSVA_1.0.1 Rgraphviz_1.30.1 RBGL_1.28.0
> [4] RColorBrewer_1.0-5 limma_3.8.3 genefilter_1.34.0
> [7] GSVAdata_0.99.0 hgu95a.db_2.5.0 org.Hs.eg.db_2.5.0
> [10] RSQLite_0.11.1 DBI_0.2-5 GSEABase_1.14.0
> [13] graph_1.30.0 annotate_1.30.1 AnnotationDbi_1.14.1
> [16] Biobase_2.12.2
>
> loaded via a namespace (and not attached):
> [1] splines_2.13.2 survival_2.36-9 tools_2.13.2 XML_3.4-2.2
> [5] xtable_1.7-0
ok, so here might be the problem, you're not using the current release
version of R with the current release version of Bioconductor packages.
so my first advice is, please update R and BioC to the current R 2.15.2
and GSVA 1.6.6.
note that had you paste the sessionInfo() output upfront, you would have
get this answer already 24 hrs before.
i hope it helps!
robert.
>>thanks for your patience,
>>
>>robert.
>>
>>>
>>> Thank you .
>>> Chuanbao
>>>
>>>
>
> I hope those details could help. Thanks.
>
> Chuanbao
>>>
>>> At 2013-02-05 16:02:58,"Robert Castelo" <robert.castelo at upf.edu> wrote:
>>>>Dear Chuanbao,
>>>>
>>>>at the first sight it looks like some problem with the installation
>>>>and/or loading of the library, since it contains some compiled C code
>>>>that is not being found when the R code is invoking it. I would need
>>>>more details to try to diagnose your problem more precisely.
>>>>
>>>>could you please:
>>>>
>>>>1. a formal aspect. i see that you've used the "Bioconductor Guest
>>>>Posting" form, if you use this way to post questions at the BioC list,
>>>>in future posts please paste your question and code in the text box code
>>>>called "Question:"
>>>>
>>>>2. please paste the output of the R command sessionInfo() in the text
>>>>box entitled "Paste the output of the R command sessionInfo() below:"
>>>>
>>>>3. show me the results of the commands:
>>>>
>>>>dim(expr) ## lookup the dimension of the expression data matrix
>>>>
>>>>expr[1:5, 1:5] ## inspect the first few cells of this matrix
>>>>
>>>>genesets ## inspect the contents of the two gene sets
>>>>
>>>>
>>>>thanks,
>>>>robert.
>>>>
>>>>On 02/05/2013 08:46 AM, Chuanbao [guest] wrote:
>>>>>
>>>>> I am a new-comer in R and am learning the Bio Package GSVA. I get the expression file and genesets from CSV files by read.csv. And when I run GSVA by gsva(expr,genesets). there is an error message. That also happened when I do as the instructions (where there are example data) tell (http://www.bioconductor.org/packages/2.11/bioc/vignettes/GSVA/inst/doc/GSVA.pdf) .
>>>>> Really appreciate your help~~~
>>>>>
>>>>> -- output of sessionInfo():
>>>>>
>>>>>
>>>>> library(GSEABase)
>>>>> library(GSVAdata)
>>>>> library(Biobase)
>>>>> library(genefilter)
>>>>> library(limma)
>>>>> library(RColorBrewer)
>>>>> library(RBGL)
>>>>> library(graph)
>>>>> library(Rgraphviz)
>>>>> library(GSVA)
>>>>> data<-read.csv(file.choose(),head=T)
>>>>> row.names(data)<-data$Symbol
>>>>> data<-data[,-1]
>>>>> expr<-data.matrix(data)
>>>>> list<-read.csv(file.choose(),head=T)
>>>>> row.names(list)<-list$Symbol
>>>>> set1<-list[1:15,1]
>>>>> set2<-list[16:30,1]
>>>>> genesets<-list(set1,set2)
>>>>> genegsva<-gsva(expr,genesets)
>>>>>
>>>>> Testing 2 gene sets.
>>>>> Computing observed enrichment scores
>>>>> Computing gene densities
>>>>> Error in .C("assess_matrix_density_R", as.double(t(expr[, sample.idxs])), :
>>>>> C symbol name "assess_matrix_density_R" not in load table
>>>>>
>>>>>
>>>>> --
>>>>> Sent via the guest posting facility at bioconductor.org.
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>
>>>>--
>>>>Robert Castelo, PhD
>>>>Associate Professor
>>>>Dept. of Experimental and Health Sciences
>>>>Universitat Pompeu Fabra (UPF)
>>>>Barcelona Biomedical Research Park (PRBB)
>>>>Dr Aiguader 88
>>>>E-08003 Barcelona, Spain
>>>>telf: +34.933.160.514
>>>>fax: +34.933.160.550
>>>
>>>
>>>
>>
>>--
>>Robert Castelo, PhD
>>Associate Professor
>>Dept. of Experimental and Health Sciences
>>Universitat Pompeu Fabra (UPF)
>>Barcelona Biomedical Research Park (PRBB)
>>Dr Aiguader 88
>>E-08003 Barcelona, Spain
>>telf: +34.933.160.514
>>fax: +34.933.160.550
>
>
>
--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550
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