converting Probs Id to gene name

Question

[Shamim Sarhadi]

Hi

I have some probe ID and I want to convert that to gene name

I've run below script in R

library("annotate")
library("rat2302.db")
select(rat2302.db, c("1368587_at", "1385248_a_at",c("SYMBOL","ENTREZID","GENENAME"))

and then I gave an error

Error in select(rat2302.db, c("1368587_at", "1385248_a_at"), c("SYMBOL",  :
  unused argument (c("SYMBOL", "ENTREZID", "GENENAME"))

Please help me, what is the problem?

Answer 1

[andrew.j.skelton73]

It's always good to expand your commands and make sure you're not missing a bracket.

select(x       = rat2302.db, 
       keys    = c("1368587_at", "1385248_a_at") ,
       columns = c("SYMBOL","ENTREZID","GENENAME"))​

[Shamim Sarhadi]

I appreciated you for your help

I run your command and also run my codes, but I gave the same error that written here

library(annotate)
library(hgu133a.db)

select(x       = hgu133a.db,
 keys    = c("209116_x_at","211696_x_at") ,
 columns = c("SYMBOL","ENTREZID","GENENAME"))

Error in select(x = hgu133a.db, keys = c("209116_x_at", "211696_x_at"),  : 
  unused arguments (keys = c("209116_x_at", "211696_x_at"), columns = c("SYMBOL", "ENTREZID", "GENENAME"))

Thank you again

[andrew.j.skelton73]

Running that code works fine for me. Run sessionInfo() and show the results.

[Shamim Sarhadi]

 sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] hgu133a.db_3.1.3     org.Hs.eg.db_3.1.2   RSQLite_1.0.0        DBI_0.3.1            annotate_1.46.0      XML_3.98-1.2
 [7] AnnotationDbi_1.30.1 Biobase_2.28.0       BiocInstaller_1.18.4 GenomicRanges_1.20.5 GenomeInfoDb_1.4.0   IRanges_2.2.4
[13] S4Vectors_0.6.0      BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] xtable_1.7-4  XVector_0.8.0 tools_3.2.1

[andrew.j.skelton73]

Maybe try appending your select command with the library you want the function to come from? AnnotationDbi::

library("annotate")
library("rat2302.db")​
AnnotationDbi::select(x       = rat2302.db, 
                      keys    = c("1368587_at", "1385248_a_at") ,
                      columns = c("SYMBOL","ENTREZID","GENENAME"))​

Note: Be careful copying code from here to your R session, sometimes line breaks are hidden and R can't interpret them.

[Shamim Sarhadi]

Thank you again and again, it works fine for me too