Question: annotation package for platform GPL2890
0
gravatar for Jing Huang
8.2 years ago by
Jing Huang380
Jing Huang380 wrote:
Dear All members, I am having a trouble to annotate a GEO data GSE8705. The platform indicated is GPL2890 GE Healthcare/Amersham Biosciences CodeLink¬ô 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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ADD COMMENTlink modified 8.2 years ago by Freudenberg, Johannes NIH/NIEHS [E]150 • written 8.2 years ago by Jing Huang380
Answer: annotation package for platform GPL2890
0
gravatar for Freudenberg, Johannes NIH/NIEHS [E]
8.2 years ago by
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 COMMENTlink written 8.2 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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 REPLYlink written 8.2 years ago by Jing Huang380
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 REPLYlink written 8.2 years ago by Sean Davis21k
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 REPLYlink written 8.2 years ago by Jing Huang380
Answer: annotation package for platform GPL2890
0
gravatar for Freudenberg, Johannes NIH/NIEHS [E]
8.2 years ago by
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 COMMENTlink written 8.2 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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 REPLYlink written 8.2 years ago by Jing Huang380
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