zhijin, Jim and Saroj: After trimmed those extra probe from probesequece file, I finally make gcrma start to work. Thank you very much for your great help. When I got those updated cdf and probesequence file, I checked and confirmed that all of probeset ID show in cdf file also show in probesequence file. But I did not check reversely. Saroj help me identify that there are extra probeset ID in probesequence file. After trimmed out those extra probeset id, I still could not make gcrma work. Dr. Wu help me identify there are some extra probe in probesequence file. (some probeset have different number of probes between cdf and probesequence file). After trimmed those extra probes, gcrma start to work. I think makeProbepackage function should do this match check. Jim: Thanks a lot for your great help. You make me have confident. From your e-mail, you make me believe that with people's help, I could solve this problem. best wish yan

Yan: I am glad that your problem is solved. Best, Saroj On Sat, September 15, 2007 2:31 pm, yzhang at vbi.vt.edu wrote: > zhijin, Jim and Saroj: > > After trimmed those extra probe from probesequece file, I finally make > gcrma start to work. Thank you very much for your great help. > > > When I got those updated cdf and probesequence file, I checked and > confirmed that all of probeset ID show in cdf file also show in > probesequence file. But I did not check reversely. Saroj help me identify > that there are extra probeset ID in probesequence file. After trimmed > out those extra probeset id, I still could not make gcrma work. Dr. Wu > help me identify there are some extra probe in probesequence file. (some > probeset have different number of probes between cdf and probesequence > file). After trimmed those extra probes, gcrma start to work. > I think makeProbepackage function should do this match check. > Jim: > Thanks a lot for your great help. You make me have confident. From your > e-mail, you make me believe that with people's help, I could solve this > problem. > > best wish yan > > _______________________________________________ > 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 > >