annotation package for platform GPL2890
2
0
Entering edit mode
Jing Huang ▴ 380
@jing-huang-4737
Last seen 10.2 years ago
Dear All members, I am having a trouble to annotate a GEO data GSE8705. The platform indicated is GPL2890 GE Healthcare/Amersham Biosciences CodeLink™ 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]]
Annotation annotate codelink Annotation annotate codelink • 2.0k views
ADD COMMENT •
0
Entering edit mode
@freudenberg-johannes-nihniehs-e-4789
Last seen 10.2 years ago
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@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]]
ADD COMMENT •
0
Entering edit mode
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="">
ADD REPLY •
0
Entering edit mode
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$PROBE_NAME),r10kcodENTREZID,ifnotfound=N A) since it looks like the keys in the r10kcod.db package are the PROBE_NAMEs. Sean >>x$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]] >> > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLY •
0
Entering edit mode
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]] >>> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >>http://news.gmane.org/gmane.science.biology.informatics.conductor >>
ADD REPLY •
0
Entering edit mode
@freudenberg-johannes-nihniehs-e-4789
Last seen 10.2 years ago
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@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]] >
ADD COMMENT •
0
Entering edit mode
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]] >> >
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 645 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6