[BioC] simpleaffy function detection.p.value (and affy function mas5call s?)

Christian.Stratowa at vie.boehringer-ingelheim.com Christian.Stratowa at vie.boehringer-ingelheim.com
Fri Mar 11 14:06:07 CET 2005

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
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

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