Dear Robert, Wolfgang and Bioconductor people, I tried to use the combineAffyBatch function, by typing > new<-combineAffyBatch(list(U133Adata, U133plus2data), c("hgu133aprobe", hgu133plusprobe"), newcdf="comb", verbose=TRUE) then it gave me: package:hgu133acdf hgu133acdf package:hgu133plus2cdf hgu133plus2cdf 24828 unique probes in common But after that the prompt never shows up, what could go wrong? Any suggestion would be appreciated. Flora

Hi Flora, "never" obviously can't be true, since to say that you would have to wait for an infinitely long time. So how long did you actually wait? Did you notice that your machine started swapping? How much memory do you have and how big are your AffyBatches? Bw Wolfgang Flora Fan wrote: > Dear Robert, Wolfgang and Bioconductor people, > > I tried to use the combineAffyBatch function, by typing > > >>new<-combineAffyBatch(list(U133Adata, U133plus2data), c("hgu133aprobe", > > hgu133plusprobe"), newcdf="comb", verbose=TRUE) > > then it gave me: > > package:hgu133acdf hgu133acdf > package:hgu133plus2cdf hgu133plus2cdf > 24828 unique probes in common > > But after that the prompt never shows up, what could go wrong? > Any suggestion would be appreciated. > > Flora > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber

Dear Flora, > So BTW, how can I run combine function at background on a > SGI machine? please read the documentation. This is all described for example in the Introduction to R "R-intro.pdf". Lots of people have spent lots of time writing this documentation, but, to paraphrase someone else, they can't read it for you. Bw Wolfgang Flora Fan wrote: > Hi Wolfgang, > > Thank you for the reply. Actually I tried one more time, and it did > finished. I have 59 affy chips and a very big memory, it took a few hours > to finish. Previously, my connection got reset before I finish my > calculations. > > Thanks, > Flora > > On Sun, 27 Feb 2005, Wolfgang Huber wrote: > > >>Hi Flora, >> >>"never" obviously can't be true, since to say that you would have to >>wait for an infinitely long time. So how long did you actually wait? Did >>you notice that your machine started swapping? How much memory do you >>have and how big are your AffyBatches? >> >> Bw >> Wolfgang >> >> >>Flora Fan wrote: >> >>>Dear Robert, Wolfgang and Bioconductor people, >>> >>>I tried to use the combineAffyBatch function, by typing >>> >>> >>> >>>>new<-combineAffyBatch(list(U133Adata, U133plus2data), c("hgu133aprobe", >>> >>>hgu133plusprobe"), newcdf="comb", verbose=TRUE) >>> >>>then it gave me: >>> >>>package:hgu133acdf hgu133acdf >>>package:hgu133plus2cdf hgu133plus2cdf >>>24828 unique probes in common >>> >>>But after that the prompt never shows up, what could go wrong? >>>Any suggestion would be appreciated. >>> >>>Flora >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor@stat.math.ethz.ch >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >>-- >>Best regards >> Wolfgang >> >>------------------------------------- >>Wolfgang Huber >>European Bioinformatics Institute >>European Molecular Biology Laboratory >>Cambridge CB10 1SD >>England >>Phone: +44 1223 494642 >>Fax: +44 1223 494486 >>Http: www.ebi.ac.uk/huber >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber