[BioC] RefSeq Entries

[Ranga Chari]

Dear Dr. Zhang, 
thank you for your suggestion.  
It is quite a problem for LocuLink IDs that have many splice forms (with different NM_ entries for one single LocusLink ID). In this case is there a method to ask only the longest form of the transcript should be written to the row linked to specific affy probe, intead of all splice forms writing to that row. 
 
thank you.
 
Kind regards
Ranga
 
 
> x2.x3.refseq.data.frame <-data.frame(refseqID,x2.x3.exp.fc,pvals.x2.x3)
Error in data.frame("1114_at" = c("NM_001202", "NP_001193", "NM_130850",  : 
        arguments imply differing number of rows: 12, 1, 4, 18, 8, 6, 2, 20, 7, 10, 16, 32, 24, 28, 5, 22, 9, 3, 40, 36, 17, 14, 42, 84, 30, 44, 34, 19, 45, 52, 13, 56, 76, 72, 11, 48, 60, 26, 21

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 


John Zhang <jzhang at jimmy.harvard.edu> wrote:

>Hello Group, 
> How can I get RefSeq accession IDs instead of LocusLink IDs. 

If you have the devel version of data package installed, you can do:

>get("1000_at", env=hgu95av2REFSEQ)
[1] "NM_002746" "NP_002737" "NM_002746" "NP_002737"

Otherwise, you have to do 
>library(reposTools)
>install.packages2("hgu95av2", develOK = TRUE)

first.

> 
>>get("1000_at", env=hguav2LOCUSID)
>[1] 5595 
>
>Instead of one single probe, how can I get all 12,625 in RefSeq accession ID 
for hguav952.
> 
>env=hguav2REFSEQ isnt working.
> 
>Please help. 
> 
>Thank you.
> 

		
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