[BioC] RefSeq Entries

[John Zhang]

>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. 

No, we annotate probes based on what LocusLink gives. I am afraid that you will 
have to figure out which of the RefSeq is the longest.

> 
>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
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>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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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084