[BioC] =?x-gbk?Q?=BB=D8=B8=B4=3ARe=3A_=5BBioC=5D_GSVA_error?=

[Robert Castelo]

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?

>  > 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?


a further fundamental piece of information i was already requesting 
below, please can you paste the output of

sessionInfo()

??

thanks for your patience,

robert.

>
> Thank you .
> 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