[BioC] biomaRt manual

[James W. MacDonald]

Hi Weiwei,

Weiwei Shi wrote:
> Sorry :) when I am composing the following email, I did not realize
> there are a couple of replies now. I read the manual carefully but I
> am still having some questions like this:
> 
> For example,
> 
> 
>>getBM(attributes=c("affy_hg_u95a", "entrezgene"), filters="affy_hg_u95a", values=head(ids2), mart=human)
> 
>   affy_hg_u95a entrezgene
> 1     31308_at         NA
> 2     31310_at       2741
> 3     31312_at       9312
> 
>>head(ids2)
> 
> [1] "31307_at"   "31308_at"   "31309_r_at" "31310_at"   "31311_at"
> [6] "31312_at"
> 
>>getBM(attributes=c("affy_hg_u95a", "entrezgene"), filters="affy_hg_u95a", values="31307_at", mart=human)
> 
> NULL
> 
> I am confused by "NULL" and "NA". I am wondering about the difference b/w them.

Steffen Durinck will know better, but I believe NULL means that Ensembl 
doesn't think that probeset maps to anything (e.g., there is nothing 
available), and NA means that there is no Entrez Gene ID for that probeset.

For instance, if you pull the Entrez Gene ID for 31307_at from the 
hgu95aENTREZID environment, it lists 9594, but if you search Entrez Gene 
for that ID it says it has been discontinued.


> 
> 
> Another question is how to make >8000 queries faster though I read
> some from previous posts.

In my experience the MySQL interface is much faster for large numbers of 
queries.

Best,

Jim


-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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