[BioC] RmiR: mapping miRNA to probe_id for Affy mogene10st

[Mary Putt]

Hi

I have data from mouse and would like to map miRNA to probeset iDs. I 
have used RmiR and get an error msg that I need to install 
RmiR.MUS.miRNA' but this annotation package does not exist. Have also 
ignored the org argument but this also yields an error.

New to this so apologies if this is a dumb ? My code follows

Many thanks in advance,

Mary Putt



 > mirnas<-data.frame(siggenes$Gene.ID)
 > mirnas$expr<-siggenes$Score.d.
 >
 >
 > genes<-data.frame(siggenes.mrna$Gene.Name)
 > genes$expr<-siggenes.mrna$Score.d.
 >
 > names(genes)<-c("genes", "expr")
 > names(mirnas)<-c("mirna", "expr")
 >  
 > dim(genes)
[1] 87  2
 > dim(mirnas)
[1] 10  2
 > genes[1:5,]
     genes      expr
1 10386996 -9.307098
2 10594609 -9.314124
3 10578017 -7.941403
4 10479625 -8.024112
5 10385995 -8.058759
 > mirnas[1:5,]
                mirna              expr
1  mmu-let-7d-star_st -3.53168874110412
2     mmu-miR-297a_st -4.60638517072762
3      mmu-miR-678_st  -3.4425261537353
4 mmu-miR-183-star_st -3.57272865665287
5      mmu-miR-223_st -3.86083950583795
 >
############
#specify MUS
##############
 > read.mir(genes = genes, mirna = mirnas, annotation = 
"mogene10sttranscriptcluster.db", id="probes", org="MUS")

Loading required package: RmiR.MUS.miRNA
Error in RmiR(genes = genes, mirna = mirna, annotation = annotation, id 
= id,  :
  RmiR.MUS.miRNA package must be installed first
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, 
logical.return = TRUE,  :
  there is no package called 'RmiR.MUS.miRNA'
 >
 > ##############
#ignore org
##################

 >read.mir(genes = genes, mirna = mirnas, annotation = 
"mogene10sttranscriptcluster.db", id="probes")

Error in `$<-.data.frame`(`*tmp*`, "mirCV", value = NA) :
  replacement has 1 rows, data has 0