Hi, In limma, how do I read a GPR file and ignore any lines whose ID column is BLANK or ""? This is my line: RG<-read.maimages(targets$FileName,source="genepix",columns=list(Gf="F 532 Median",Gb="B532 Median",Rf="F635 Median",Rb="B635 Median")) Thanks! G

What I do is to read in everything and then give weight 0 to these lines. --Naomi At 12:27 PM 7/18/2005, Guoneng Zhong wrote: >Hi, > >In limma, how do I read a GPR file and ignore any lines whose ID column >is BLANK or ""? > >This is my line: > >RG<-read.maimages(targets$FileName,source="genepix",columns=list(Gf=" F532 >Median",Gb="B532 Median",Rf="F635 Median",Rb="B635 Median")) > >Thanks! >G > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

Hi, What I do is to read everything, create a spottypes.txt file (limma users guide pag. 12) to identify the lines in the GPR files according to the Name or ID column, and then remove those which match certain label. For example (assume in the spottypes file you label "blank" the lines with ID BLANK or '"), then you could do: RG <- read.maimages(targets$Filename, source = "genepix", columns = columns) spottypes <- readSpotTypes() RG$genes$Status<-controlStatus(spottypes,RG) RG <- RG[RG$genes$Status != "blank",] Hope this helps, Lourdes > What I do is to read in everything and then give weight 0 to these lines. > > --Naomi > > At 12:27 PM 7/18/2005, Guoneng Zhong wrote: > >Hi, > > > >In limma, how do I read a GPR file and ignore any lines whose ID column > >is BLANK or ""? > > > >This is my line: > > > >RG<-read.maimages(targets$FileName,source="genepix",columns=list(Gf ="F532 > >Median",Gb="B532 Median",Rf="F635 Median",Rb="B635 Median")) > > > >Thanks! > >G > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Bioinformatics Consulting Center > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111