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Question: Newbie Illumina Probe Annotation (beadarray) Problem
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gravatar for LeeH
9.7 years ago by
LeeH10
LeeH10 wrote:
Hi all, I've been given an illumina dataset to process and have hit a bit of a stumbling block adding in probe annotation using beadarray. The chip used was the Illumina mouseRef-8 v1.1 expression beadchip. However, all i have is the summary level data, annotated with probeids of the form "ILMN_nnnnnn" & thats it. I've read as much documentation as i can get my hands on but still havent managed to add in annotations, such as refseq IDs etc. I've downloaded the various dbs and run annotations but all i get is the default of NA.I looked into the probe tables using dbGetQuery and couldnt see anywhere that i could map to ILMN_ ID's but I've never used this before & so could well be missing something. If anyone could point me in the direction it would be incredibly helpful. cheers [[alternative HTML version deleted]]
ADD COMMENTlink modified 9.7 years ago by Priscila Darakjian40 • written 9.7 years ago by LeeH10
0
gravatar for Priscila Darakjian
9.7 years ago by
Priscila Darakjian40 wrote:
Look at http://www.switchtoi.com/annotationprevfiles.ilmn I believe you will be interested specifically in either of these two files: MouseRef-8_V1_1_R3_11234312_A.bgx (this is revision 3) MouseRef-8_V1_1_R1_11234312_A.bgx Good luck, Priscila -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of LeeH Sent: Wednesday, January 28, 2009 2:50 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Newbie Illumina Probe Annotation (beadarray) Problem Hi all, I've been given an illumina dataset to process and have hit a bit of a stumbling block adding in probe annotation using beadarray. The chip used was the Illumina mouseRef-8 v1.1 expression beadchip. However, all i have is the summary level data, annotated with probeids of the form "ILMN_nnnnnn" & thats it. I've read as much documentation as i can get my hands on but still havent managed to add in annotations, such as refseq IDs etc. I've downloaded the various dbs and run annotations but all i get is the default of NA.I looked into the probe tables using dbGetQuery and couldnt see anywhere that i could map to ILMN_ ID's but I've never used this before & so could well be missing something. If anyone could point me in the direction it would be incredibly helpful. cheers [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 9.7 years ago by Priscila Darakjian40
Actually, I would look at MouseRef-8_V1_1_R3_11234312_A.bgx (this probably has some annotation changes that were not present in R1) -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Priscila Darakjian Sent: Thursday, January 29, 2009 9:30 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Newbie Illumina Probe Annotation (beadarray) Problem Look at http://www.switchtoi.com/annotationprevfiles.ilmn I believe you will be interested specifically in either of these two files: MouseRef-8_V1_1_R3_11234312_A.bgx (this is revision 3) MouseRef-8_V1_1_R1_11234312_A.bgx Good luck, Priscila -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of LeeH Sent: Wednesday, January 28, 2009 2:50 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Newbie Illumina Probe Annotation (beadarray) Problem Hi all, I've been given an illumina dataset to process and have hit a bit of a stumbling block adding in probe annotation using beadarray. The chip used was the Illumina mouseRef-8 v1.1 expression beadchip. However, all i have is the summary level data, annotated with probeids of the form "ILMN_nnnnnn" & thats it. I've read as much documentation as i can get my hands on but still havent managed to add in annotations, such as refseq IDs etc. I've downloaded the various dbs and run annotations but all i get is the default of NA.I looked into the probe tables using dbGetQuery and couldnt see anywhere that i could map to ILMN_ ID's but I've never used this before & so could well be missing something. If anyone could point me in the direction it would be incredibly helpful. cheers [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 9.7 years ago by Priscila Darakjian40
One of the problems is that Illumina has changed the format of its identifiers. Perhaps the illuminaMousev1p1.db package should be changed to use the "ILMN_" type identifiers. Lynn Amon Priscila Darakjian wrote: > Actually, I would look at MouseRef-8_V1_1_R3_11234312_A.bgx (this probably has some annotation changes that were not present in R1) > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto :bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Priscila Darakjian > Sent: Thursday, January 29, 2009 9:30 AM > To: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Newbie Illumina Probe Annotation (beadarray) Problem > > Look at http://www.switchtoi.com/annotationprevfiles.ilmn > I believe you will be interested specifically in either of these two files: > MouseRef-8_V1_1_R3_11234312_A.bgx (this is revision 3) > MouseRef-8_V1_1_R1_11234312_A.bgx > > Good luck, > > Priscila > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto :bioconductor-bounces at stat.math.ethz.ch] On Behalf Of LeeH > Sent: Wednesday, January 28, 2009 2:50 AM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Newbie Illumina Probe Annotation (beadarray) Problem > > Hi all, I've been given an illumina dataset to process and have hit a bit of > a stumbling block adding in probe annotation using beadarray. The chip used > was the Illumina mouseRef-8 v1.1 expression beadchip. However, all i have is > the summary level data, annotated with probeids of the form "ILMN_nnnnnn" & > thats it. I've read as much documentation as i can get my hands on but still > havent managed to add in annotations, such as refseq IDs etc. I've > downloaded the various dbs and run annotations but all i get is the default > of NA.I looked into the probe tables using dbGetQuery and couldnt see > anywhere that i could map to ILMN_ ID's but I've never used this before & so > could well be missing something. > > If anyone could point me in the direction it would be incredibly helpful. > cheers > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 9.7 years ago by Lynn Amon280
I haven't used the illuminaMousev1p1.db. However, and maybe this might help you to go in the right direction, the Illumina annotation files have a column named "Probe_ID." This id is supposed to identify the specific probe sequence across arrays (if you compare across arrays you will see that, for a specific Probe_ID, the sequence in the various arrays is the same . These ids start also with ILM_, but are not the same as the "Transcript" id column. So, the only ID I see that can compare apples to apples across arrays is the Probe_ID. The "Transcript" (which has the same format as ILM_nnnnnn) and "Array_Address_ID" (which is just a 6 or 7 digit number) columns are specific to the particular array in question and cannot be used for comparisons across different arrays (they will be pointing to different probes). It might be that the package is expecting a different ID from the one you have for that specific array. So you might have to replace the Ids you have with one of the other ones to identify the probes through the package. Look at the annotation file and see which ID the dataset you have is using. Priscila -----Original Message----- From: Lynn Amon [mailto:lamon@fhcrc.org] Sent: Thursday, January 29, 2009 9:55 AM To: Priscila Darakjian Cc: bioconductor at stat.math.ethz.ch; Mark Dunning Subject: Re: [BioC] Newbie Illumina Probe Annotation (beadarray) Problem One of the problems is that Illumina has changed the format of its identifiers. Perhaps the illuminaMousev1p1.db package should be changed to use the "ILMN_" type identifiers. Lynn Amon Priscila Darakjian wrote: > Actually, I would look at MouseRef-8_V1_1_R3_11234312_A.bgx (this probably has some annotation changes that were not present in R1) > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto :bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Priscila Darakjian > Sent: Thursday, January 29, 2009 9:30 AM > To: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Newbie Illumina Probe Annotation (beadarray) Problem > > Look at http://www.switchtoi.com/annotationprevfiles.ilmn > I believe you will be interested specifically in either of these two files: > MouseRef-8_V1_1_R3_11234312_A.bgx (this is revision 3) > MouseRef-8_V1_1_R1_11234312_A.bgx > > Good luck, > > Priscila > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto :bioconductor-bounces at stat.math.ethz.ch] On Behalf Of LeeH > Sent: Wednesday, January 28, 2009 2:50 AM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Newbie Illumina Probe Annotation (beadarray) Problem > > Hi all, I've been given an illumina dataset to process and have hit a bit of > a stumbling block adding in probe annotation using beadarray. The chip used > was the Illumina mouseRef-8 v1.1 expression beadchip. However, all i have is > the summary level data, annotated with probeids of the form "ILMN_nnnnnn" & > thats it. I've read as much documentation as i can get my hands on but still > havent managed to add in annotations, such as refseq IDs etc. I've > downloaded the various dbs and run annotations but all i get is the default > of NA.I looked into the probe tables using dbGetQuery and couldnt see > anywhere that i could map to ILMN_ ID's but I've never used this before & so > could well be missing something. > > If anyone could point me in the direction it would be incredibly helpful. > cheers > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 9.7 years ago by Priscila Darakjian40
0
gravatar for Wei Shi
9.7 years ago by
Wei Shi2.9k
Australia
Wei Shi2.9k wrote:
Have you looked at the Illumina annotation file which I am sure contains the annotation for your probeids? Wei LeeH wrote: > Hi all, I've been given an illumina dataset to process and have hit a bit of > a stumbling block adding in probe annotation using beadarray. The chip used > was the Illumina mouseRef-8 v1.1 expression beadchip. However, all i have is > the summary level data, annotated with probeids of the form "ILMN_nnnnnn" & > thats it. I've read as much documentation as i can get my hands on but still > havent managed to add in annotations, such as refseq IDs etc. I've > downloaded the various dbs and run annotations but all i get is the default > of NA.I looked into the probe tables using dbGetQuery and couldnt see > anywhere that i could map to ILMN_ ID's but I've never used this before & so > could well be missing something. > > If anyone could point me in the direction it would be incredibly helpful. > cheers > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 9.7 years ago by Wei Shi2.9k
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