Question: Mapping Agilent Probes
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gravatar for peter robinson
10.4 years ago by
peter robinson300 wrote:
Dear 'conductors, I am trying to get a mapping from Agilent mouse microarray probes to ENSEMBL gene ids for further analysis. >library("mgug4122a.db") >data = "path to data" ## This is data produced from an initial analysis of an Agilent hybridization >dat <-read.table(data,sep=",",header=TRUE) >pro = as.character(dat[,3]) ### The Agilent probe names > head(pro) [1] "A_52_P616356" "A_52_P580582" "A_52_P403405" "A_52_P819156" "A_51_P331831" [6] "A_51_P430630" >ens = unlist(mget(pro,mgug4122aENSEMBL)) >map.dat = merge(dat,ens,by=intersect(dat[,3],names(ens)),all.x=TRUE,all.y=FALSE) Fehler in fix.by(by.x, x) : 'by' muss g?ltige Spalte(n) spezifizieren Thus I get an error stating that 'by' needs to specify a valid column. My goal is to create a table that I can output that will contain the original information as well as the mapping to ENSEMBL in the correct rows. Also, what is the meaning of ENSEMBL2probe in the "mgug4122a.db" package? Is it worrisome that there seems to be an ENSEMBL id for only about 80% of the Agilent probes? Is there any way of getting more mappings? (I am aware that many of the probes are controls). THanks Peter
microarray probe • 1.9k views
ADD COMMENTlink modified 10.3 years ago by MartenJäger40 • written 10.4 years ago by peter robinson300
Answer: Mapping Agilent Probes
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gravatar for MartenJäger
10.3 years ago by
MartenJäger40
MartenJäger40 wrote:
Hi Peter, you can use the annotate package: >library("annotate") >library("mgug4122a.db") >AGI_ID = c("A_52_P616356", "A_52_P580582", "A_52_P403405", "A_52_P819156", "A_51_P331831", "A_51_P430630") >agi.ens = lookUp(AGI_ID, "mgug4122a.db", "ENSEMBL") This will return you a list with the Ensembl GeneIDs in the correct order like in AGI_ID. For AGI_IDs with no corresponding Ensembl geneID you will get a "NA". I hope this will solve your Problem. Marten > Dear 'conductors, > > I am trying to get a mapping from Agilent mouse microarray probes to > ENSEMBL gene ids for further analysis. > > >library("mgug4122a.db") > >data = "path to data" ## This is data produced from an initial > analysis of an Agilent hybridization > >dat <-read.table(data,sep=",",header=TRUE) > >pro = as.character(dat[,3]) ### The Agilent probe names > > > head(pro) > [1] "A_52_P616356" "A_52_P580582" "A_52_P403405" "A_52_P819156" > "A_51_P331831" > [6] "A_51_P430630" > > > >ens = unlist(mget(pro,mgug4122aENSEMBL)) > > >map.dat = > merge(dat,ens,by=intersect(dat[,3],names(ens)),all.x=TRUE,all.y=FALSE) > Fehler in fix.by(by.x, x) : 'by' muss g?ltige Spalte(n) spezifizieren > > Thus I get an error stating that 'by' needs to specify a valid column. > > > My goal is to create a table that I can output that will contain the > original information as well as the mapping to ENSEMBL in the correct > rows. > > Also, what is the meaning of ENSEMBL2probe in the "mgug4122a.db" > package? > > Is it worrisome that there seems to be an ENSEMBL id for only about > 80% of the Agilent probes? Is there any way of getting more mappings? > (I am aware that many of the probes are controls). > > THanks Peter > > _______________________________________________ > 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 10.3 years ago by MartenJäger40
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