[BioC] annotation package for platform GPL2890

[Freudenberg, Johannes (NIH/NIEHS) [E]]

Based on the file you sent, it looks like the IDs you're trying to match do not correspond to the keys in the table.  

> head(toTable(r10kcodENTREZID))
  probe_id gene_id
1   GE1071   64507
2   GE1072   79245
3   GE1073   50693
4   GE1075  117045
5   GE1076  171150
6   GE1077   81682


Please try "PROBE_NAME" instead as in:

>x$ENTREZ=toTable(y)[match(x$ PROBE_NAME,toTable(y)[, 1]), 2]

Best regards,
--Johannes


-----Original Message-----
From: Jing Huang [mailto:huangji at ohsu.edu] 
Sent: Tuesday, September 20, 2011 1:33 PM
To: Freudenberg, Johannes (NIH/NIEHS) [E]; bioconductor at r-project.org
Subject: Re: annotation package for platform GPL2890

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()
>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
>
>
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