[BioC] annotation package for platform GPL2890

[Jing Huang]

Dear Sean,

I have tried it. It works.

Many Thanks

Jing

On 9/22/11 12:05 PM, "Sean Davis" <sdavis2 at mail.nih.gov> wrote:

>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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