Question: mapping probe sets from yeast2 array to probe sets in hgu133A
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gravatar for Glazko, Galina
8.9 years ago by
Glazko, Galina350 wrote:
Dear List, I would appreciate if someone could indicate the easy way how to map probe sets from yeast2 array onto hgu133a probe sets in Bioconductor; May be throughout BioMart? (Mapping should be based on orthologs). I know how to do it in NetAffx, Affymetrix but it takes too much time. Thank you! Best regards Galina [[alternative HTML version deleted]]
hgu133a yeast2 probe • 557 views
ADD COMMENTlink modified 8.9 years ago by Alexandre Kuhn60 • written 8.9 years ago by Glazko, Galina350
Answer: mapping probe sets from yeast2 array to probe sets in hgu133A
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gravatar for Peter Bazeley
8.9 years ago by
Peter Bazeley50 wrote:
Hi Galina, Perhaps the annotationTools package. Regards, Pete On Thu, Aug 5, 2010 at 2:42 PM, Glazko, Galina < Galina_Glazko@urmc.rochester.edu> wrote: > Dear List, > > I would appreciate if someone could indicate the easy way how to map probe > sets from yeast2 array onto hgu133a probe sets in Bioconductor; > May be throughout BioMart? > (Mapping should be based on orthologs). > > I know how to do it in NetAffx, Affymetrix but it takes too much time. > Thank you! > > Best regards > Galina > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 8.9 years ago by Peter Bazeley50
Answer: mapping probe sets from yeast2 array to probe sets in hgu133A
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gravatar for James W. MacDonald
8.9 years ago by
United States
James W. MacDonald50k wrote:
Hi Galina, See ?idConverter in the AnnotationDbi package. You will have to do some extra work converting from yeast2 probe IDs to hgu133a probe IDs, but that is trivial. Best, Jim On 8/5/10 2:42 PM, Glazko, Galina wrote: > Dear List, > > I would appreciate if someone could indicate the easy way how to map probe > sets from yeast2 array onto hgu133a probe sets in Bioconductor; > May be throughout BioMart? > (Mapping should be based on orthologs). > > I know how to do it in NetAffx, Affymetrix but it takes too much time. > Thank you! > > Best regards > Galina > > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENTlink written 8.9 years ago by James W. MacDonald50k
Jim, Thank you for the answer. I would appreciate if you could describe the 'trivial' step: "converting from yeast2 probe IDs to hgu133a probe IDs"? It is not obvious for me, sorry. Best regards Galina -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Friday, August 06, 2010 12:10 PM To: Glazko, Galina Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A Hi Galina, See ?idConverter in the AnnotationDbi package. You will have to do some extra work converting from yeast2 probe IDs to hgu133a probe IDs, but that is trivial. Best, Jim On 8/5/10 2:42 PM, Glazko, Galina wrote: > Dear List, > > I would appreciate if someone could indicate the easy way how to map probe > sets from yeast2 array onto hgu133a probe sets in Bioconductor; > May be throughout BioMart? > (Mapping should be based on orthologs). > > I know how to do it in NetAffx, Affymetrix but it takes too much time. > Thank you! > > Best regards > Galina > > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD REPLYlink written 8.9 years ago by Glazko, Galina350
Hi Galina, The trivial step is converting from yeast2 probe IDs to say, ENSEMBL IDs, and then converting e.g., Entrez Gene IDs to hgu133a probe IDs. But you seem lost, so here is a full example: > library(yeast2.db) > ids <- Rkeys(yeast2ENSEMBL) ## you could use other ids as well, I suppose > length(ids) [1] 5883 > egids <- idConverter(ids, "SACCE","HOMSA","ENSEMBL") Loading required package: hom.Sc.inp.db Loading required package: org.Hs.eg.db > length(egids) [1] 1505 > class(egids) [1] "list" > table(sapply(egids, length)) 1 2 3 13 1459 41 4 1 ## so 1505 things were converted, most 1-1. > library(hgu133a.db) > hguids <- mget(unlist(egids), revmap(hgu133aENTREZID)) > length(hguids) [1] 1566 > table(sapply(hguids, length)) 1 2 3 4 5 6 7 9 1040 303 147 54 16 4 1 1 > hguids[1:10] $`4512` [1] NA $`4508` [1] NA $`4519` [1] NA $`4513` [1] NA $`100289404` [1] NA $`100292744` [1] NA $`23355` [1] "209553_at" $`3312` [1] "208687_x_at" "210338_s_at" "221891_x_at" $`4913` [1] "209731_at" $`5519` [1] "202883_s_at" "202884_s_at" "202885_s_at" "202886_s_at" "222351_at" So this will give you all the homologous probesets on the HGU133a chip. If you want to know which yeast2 probeset ID maps to a given HGU133a probeset, you will have to do some extra work tracking the names. Best, Jim On 8/6/10 2:06 PM, Glazko, Galina wrote: > Jim, > > Thank you for the answer. > I would appreciate if you could describe the 'trivial' step: > "converting from yeast2 probe IDs to hgu133a probe IDs"? > It is not obvious for me, sorry. > > Best regards > Galina > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: Friday, August 06, 2010 12:10 PM > To: Glazko, Galina > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A > > Hi Galina, > > See ?idConverter in the AnnotationDbi package. You will have to do some > extra work converting from yeast2 probe IDs to hgu133a probe IDs, but > that is trivial. > > Best, > > Jim > > > > On 8/5/10 2:42 PM, Glazko, Galina wrote: >> Dear List, >> >> I would appreciate if someone could indicate the easy way how to map probe >> sets from yeast2 array onto hgu133a probe sets in Bioconductor; >> May be throughout BioMart? >> (Mapping should be based on orthologs). >> >> I know how to do it in NetAffx, Affymetrix but it takes too much time. >> Thank you! >> >> Best regards >> Galina >> >> >> [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD REPLYlink written 8.9 years ago by James W. MacDonald50k
Answer: mapping probe sets from yeast2 array to probe sets in hgu133A
0
gravatar for Alexandre Kuhn
8.9 years ago by
Alexandre Kuhn60 wrote:
Hi Galina, you can use the function ps2ps in the package annotationTools. You will only need to download the Affymetrix annotation files corresponding to your microarrays of interest, as well as the HomoloGene database (see FTP site on http://www.ncbi.nlm.nih.gov/homologene). You can then do annotYeast <- read.csv('Yeast_2.na30.annot.csv',colClasses='character',comment.char= '#') annotHuman <- read.csv('HG- U133A.na30.annot.csv',colClasses='character',comment.char='#') homologene <- read.delim('homologene_build64.data',header=FALSE) homoSapiens_ID <- 9606 mappingTable <- ps2ps(annotYeast,annotHuman,homologene,homoSapiens_ID) Alternatively, if you want to make use of the probe set mapping provided by Affymetrix, you can also use the function getHOMOLOG to mine the corresponding file affyOrthologs <- read.csv("Yeast_2.na30.ortholog.csv",colClasses='character') allps <- annotYeast[,1] affyMap <- getHOMOLOG(allps,'HG- U133A',affyOrthologs,cluster=TRUE,clusterCol=1,speciesC ol=4,idCol=3) In this particular yeast to human mapping, the number of human ortholog probe sets found with the Affymetrix ortholog file (2656) is much higher than with ps2ps (1405). The reason seems to be that some probe sets have an empty "Entrez gene ID" entry in the Yeast2 annotation file (gene symbols are present though). This prevents ps2ps from mapping these probe sets since it uses Entrez gene IDs to find orthologs in HomoloGene. Alexandre > -----Original Message----- > From: Glazko, Galina [mailto:Galina_Glazko at urmc.rochester.edu] > Sent: Thursday, August 05, 2010 2:42 PM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] mapping probe sets from yeast2 array to probe sets in > hgu133A > > Dear List, > > I would appreciate if someone could indicate the easy way how to map > probe > sets from yeast2 array onto hgu133a probe sets in Bioconductor; > May be throughout BioMart? > (Mapping should be based on orthologs). > > I know how to do it in NetAffx, Affymetrix but it takes too much time. > Thank you! > > Best regards > Galina > > > [[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 8.9 years ago by Alexandre Kuhn60
Dear Alexandre, James and list thank you very much for your helpful advises! Alexandre, I am very grateful for these mappings, best Galina ________________________________________ From: Alexandre Kuhn [kuhnam@mail.nih.gov] Sent: Tuesday, August 10, 2010 6:00 PM To: Glazko, Galina; bioconductor at stat.math.ethz.ch Subject: RE: [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A Hi Galina, you can use the function ps2ps in the package annotationTools. You will only need to download the Affymetrix annotation files corresponding to your microarrays of interest, as well as the HomoloGene database (see FTP site on http://www.ncbi.nlm.nih.gov/homologene). You can then do annotYeast <- read.csv('Yeast_2.na30.annot.csv',colClasses='character',comment.char= '#') annotHuman <- read.csv('HG- U133A.na30.annot.csv',colClasses='character',comment.char='#') homologene <- read.delim('homologene_build64.data',header=FALSE) homoSapiens_ID <- 9606 mappingTable <- ps2ps(annotYeast,annotHuman,homologene,homoSapiens_ID) Alternatively, if you want to make use of the probe set mapping provided by Affymetrix, you can also use the function getHOMOLOG to mine the corresponding file affyOrthologs <- read.csv("Yeast_2.na30.ortholog.csv",colClasses='character') allps <- annotYeast[,1] affyMap <- getHOMOLOG(allps,'HG- U133A',affyOrthologs,cluster=TRUE,clusterCol=1,speciesC ol=4,idCol=3) In this particular yeast to human mapping, the number of human ortholog probe sets found with the Affymetrix ortholog file (2656) is much higher than with ps2ps (1405). The reason seems to be that some probe sets have an empty "Entrez gene ID" entry in the Yeast2 annotation file (gene symbols are present though). This prevents ps2ps from mapping these probe sets since it uses Entrez gene IDs to find orthologs in HomoloGene. Alexandre > -----Original Message----- > From: Glazko, Galina [mailto:Galina_Glazko at urmc.rochester.edu] > Sent: Thursday, August 05, 2010 2:42 PM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] mapping probe sets from yeast2 array to probe sets in > hgu133A > > Dear List, > > I would appreciate if someone could indicate the easy way how to map > probe > sets from yeast2 array onto hgu133a probe sets in Bioconductor; > May be throughout BioMart? > (Mapping should be based on orthologs). > > I know how to do it in NetAffx, Affymetrix but it takes too much time. > Thank you! > > Best regards > Galina > > > [[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 REPLYlink written 8.9 years ago by Glazko, Galina350
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