[BioC] multiple annotations with get()?

[James W. MacDonald]

You might also consider using select(), which is the newfangled way to 
do things:

> z <- c("SFRP2","MGP","COL10A1","MSRB3")
> select(org.Hs.eg.db, z, "ENTREZID","SYMBOL")
   SYMBOL ENTREZID
1   SFRP2     6423
2     MGP     4256
3 COL10A1     1300
4   MSRB3   253827

Best,

Jim

On Friday, October 11, 2013 3:34:45 PM, Sean Davis wrote:
> On Fri, Oct 11, 2013 at 3:31 PM, Ed Siefker <ebs15242 at gmail.com> wrote:
>> I have a list of gene symbols I want to convert into entrez ids.
>> For example, I have a txt file with these symbols:
>>
>> SFRP2
>> MGP
>> COL10A1
>> MSRB3
>>
>> I've loaded Biobase, annotate, and org.Hs.eg.db and done the following:
>>
>> symb<- read.table("example.txt",stringsAsFactors=FALSE)
>>> get(symb, org.Hs.egSYMBOL2EG)
>
> Hi, Ed.
>
> You may want to use mget (multiple get) instead.
>
> Sean
>
>> Error in .checkKeysAreWellFormed(keys) :
>>    keys must be supplied in a character vector with no NAs
>>> class(symb[[1]])
>> [1] "character"
>>> length(symb[[1]])
>> [1] 4
>>> get(symb[[1]], org.Hs.egSYMBOL2EG)
>> [1] "6423"
>>
>> Why is get() only giving me one entrez ID?  Shouldn't it give me a vector
>> of 4 entrez IDs when I pass it a vector of 4 gene symbols?
>>
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>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099