[BioC] annotation package for platform GPL2890
Jing Huang
huangji at ohsu.edu
Tue Sep 20 19:32:52 CEST 2011
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]]
>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: LUSH30D - LUIH30D.txt
URL: <https://stat.ethz.ch/pipermail/bioconductor/attachments/20110920/e51f929c/attachment-0001.txt>
More information about the Bioconductor
mailing list