[BioC] annotation package for platform GPL2890

[Sean Davis]

On Tue, Sep 20, 2011 at 1:32 PM, Jing Huang <huangji at ohsu.edu> wrote:
> Thank you Johannes.
>
> I attached the topTable that I generated from GEO8705. I am trying to
> annotate the table with R r10kcod.db. It didn't work. Here is my R:
>
>> source("http://www.bioconductor.org/biocLite.R")
>> biocLite("r10kcod.db")
>
>> library(r10kcod.db)
>>r10kcod()
>>y=r10kcodENTREZID
>>x=topTable()

Try:

entrezids=mget(as.character(x$PROBE_NAME),r10kcodENTREZID,ifnotfound=NA)

since it looks like the keys in the r10kcod.db package are the PROBE_NAMEs.

Sean


>>x$ENTREZ=toTable(y)[match(x$ID,toTable(y)[, 1]), 2]
>>head(x)
>  ID LOGICAL_ROW LOGICAL_COL PROBE_NAME PROBE_TYPE PUB_PROBE_TARGETS
> SPOT_ID      GB_ACC       GI     GB_LIST  GI_LIST     logFC   AveExpr
>   t      P.Value
> 1388  3215          32          15    GE12861  DISCOVERY            SINGLE
>         BG373142.1 13269679  BG373142.1 13269679 -1.218464 10.823167
> -6.613231 1.949953e-07
> 867   2048          20          48    GE13606  DISCOVERY            SINGLE
>         AI007974.1  3221806  AI007974.1  3221806 -1.926262  6.878387
> -6.427029 3.311469e-07
> 9637 21544         215          44    GE21624  DISCOVERY            SINGLE
>           D89965.1  1772461    D89965.1  1772461  0.191256  4.290006
> 6.340659 4.237440e-07
> 1466  3348          33          48    GE13804  DISCOVERY            SINGLE
>         AI045904.1  3292723  AI045904.1  3292723 -2.691548  8.767649
> -6.262723 5.295824e-07
> 373   1004          10           4    GE13407  DISCOVERY            SINGLE
>        NM_030858.1 13540678 NM_030858.1 13540678 -2.435262  8.143696
> -6.232923 5.767741e-07
> 8290 18608         186           8    GE18381  DISCOVERY            SINGLE
>         BE116089.1  8508194  BE116089.1  8508194 -1.768631  7.447167
> -6.020654 1.061160e-06
>       adj.P.Val        B              ENTREZ
> 1388 0.001155163 7.031935   <NA>
> 867  0.001155163 6.551450   <NA>
> 9637 0.001155163 6.327397   <NA>
> 1466 0.001155163 6.124616   <NA>
> 373  0.001155163 6.046936   <NA>
> 8290 0.001519451 5.491476   <NA>
>
> There is no ENTREZ match to the table
>
> MANY MANY Thanks
>
> Jing
>
>
>
> On 9/20/11 10:22 AM, "Freudenberg, Johannes (NIH/NIEHS) [E]"
> <johannes.freudenberg at nih.gov> wrote:
>
>>Dear Jing,
>>
>>I couldn't find any problems with r10kcod.db.  Can you please be more
>>specific as to what exactly the trouble is?
>>
>>Best,
>>--Johannes
>>
>>
>>-----Original Message-----
>>From: Jing Huang [mailto:huangji at ohsu.edu]
>>Sent: Tuesday, September 20, 2011 1:00 PM
>>To: bioconductor at r-project.org
>>Subject: [BioC] annotation package for platform GPL2890
>>
>>Dear All members,
>>
>>I am having a trouble to annotate a GEO data GSE8705. The platform
>>indicated is GPL2890 GE Healthcare/Amersham Biosciences CodeLink(tm)
>>UniSet Rat I Bioarray.
>>
>>I have tried to annotate the topTable with R annotation package
>>r10kcod.db, which is for GE CodeLink UniSet Rat I Bioarray (~10 000 rat
>>gene targets) annotation data (chip r10kcod). But it didn't work.
>>
>>Can somebody advise?
>>
>>Many Thanks
>>
>>Jing
>>
>>
>>       [[alternative HTML version deleted]]
>>
>
>
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