

Thanks, Robert.
Comments below as well.






At 2013-02-07 18:27:38,"Robert Castelo" <robert.castelo@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. 

>>  > 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   

>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@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@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

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