Dear BioC people Comparing the output from simpleaffy with the Affymetrix MAS5 software we have found the following inconsistency: Output MAS5: MAS5 Signal Detection Detection p-value 1005_at 80139.8 P 0.000219 1081_at 24695.2 P 0.000219 AFFX-BioB-3_at 12714.9 P 0.00011 AFFX-BioB-M_at 21123.8 P 0.000044 AFFX-BioC-3_at 19104.8 P 0.000052 AFFX-BioC-5_at 22924.5 P 0.000095 AFFX-BioDn-3_at 124659.3 P 0.000081 Output from simpleaffy (combining output from functions call.exprs and detection.p.value): BioC Signal Detection Detection p-value 1005_at 80197.83231 P 0.000218932 1081_at 24713.12704 P 0.000218932 AFFX-BioB-3_at 12724.08753 P 0.00010957 AFFX-BioB-M_at 21139.08669 A 4.43E-05 AFFX-BioC-3_at 19118.62503 A 5.17E-05 AFFX-BioC-5_at 22941.10276 A 9.45E-05 AFFX-BioDn-3_at 124749.6972 A 8.15E-05 Comparing the two tables you see that simpleaffy gives an Absent call whenever the detection p-vaule is of type "n.nE-0x" Could it be that in function detection.p.value the statement: calls <- sapply(p, function(y)... should be replaced with: calls <- sapply(as.double(p), function(y)... For your info: We are using R-2.0.1 and simpleaffy_2.01 on an 64bit Opteron Machine with RedHat Enterprise 3.0 Thank you in advance for your help Best regards Christian Stratowa