[BioC] annotation package for platform GPL2890

[Jing Huang]

THANK YOU SO MUCH Johannes. Both works!! I have learned something new.

Jing

On 9/20/11 10:47 AM, "Freudenberg, Johannes (NIH/NIEHS) [E]"
<johannes.freudenberg at nih.gov> wrote:

>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
>>
>>
>>	[[alternative HTML version deleted]]
>>
>