I have seem to run into an error when running qc.stats on affy moe430 2 arrays. > qc <- qc.stats(gclmko.raw,gclmko.mas5) Getting probe level data... Computing p-values Doing PMA Calls Error in qc.stats(gclmko.raw, gclmko.mas5) : Sorry - I'm afraid I don't know about the spike probes on ' mouse4302cdf ' arrays. base 1.9.0 utils 1.9.0 graphics 1.9.0 stats 1.9.0 methods 1.9.0 affy 1.4.21 Biobase 1.4.10 tools 1.9.0 gcrma 1.0.6 simpleaffy 1.09 mouse4302cdf 1.4.1 Thanks, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html

Hi Dick, I had the same problem, and also with drosophila arrays. If you take a look at the code for the function qc.stats, it doesn't include descriptions for the moe430 chips or drosophila, you can edit the else: else { if (n %in% c("rae230acdf")) { rats <- 2^cbind((x["AFFX_Rat_GAPDH_3_at",] - x["AFFX_Rat_GAPDH_5_at",]), (x["AFFX_Rat_GAPDH_3_at",] - x["AFFX_Rat_GAPDH_M_at",]), (x["AFFX_Rat_beta-actin_3_at",] - x["AFFX_Rat_beta-actin_5_at",]), (x["AFFX_Rat_beta-actin_3_at",] - x["AFFX_Rat_beta-actin_5_at",])); } by the way, I think the last line in the function above should probably be AFFX_Rat_beta-actin_M_at" for rat chip users. to include your moe430 using the rat chip as a template, else { if (n %in% c("moe4302cdf(or whatever your version is)")) { rats <- 2^cbind((x["AFFX-GapdhMur/M32599_3_at",] - x["AFFX-GapdhMur/M32599_5_at",]), (x["AFFX-GapdhMur/M32599_3_at",] - x["AFFX-GapdhMur/M32599_M_at",]), (x["AFFX-b-ActinMur/M12481_3_at",] - x["AFFX-b-ActinMur/M12481_5_at",]), (x["AFFX-b-ActinMur/M12481_3_at",] - x["AFFX-b-ActinMur/M12481_M_at",])); } just be sure to include the correct descriptions for the controls on the chip. Leave the rats object alone, because everything refers to rats. Rename the function something like qc2.stats and you should be able to get it working with your chips. Best, mike Michael McDonald Ph.D. Duboule Lab Universite de Geneve Quai Ernest-Ansermet 30 Geneve 1211 Switzerland 41 22 379 67 79 41 22 379 67 95 fax