[BioC] Negative Values (?!) loaded by affy package from CEL file of MOE430A

[Simon Lin]

Hello,

I loaded a few CEL file from MOE430A experiments. Strangely, many PM 
values are negative! As a result, RMA and other routines did not work.

Any ideas?? See scripts below. I am puzzled!

I am running Bioconductor 1.6, R 2.1.0, with moe430acdf loaded.

Thanks!

Simon
################################################################

 > result.batch<- ReadAffy(filenames=CEL.fileNames)

 > result.batch
AffyBatch object
size of arrays=712x712 features (11886 kb)
cdf=MOE430A (22690 affyids)
number of samples=3
number of genes=22690
annotation=moe430a
 >

 > x<-pm (result.batch)
 > dim (x)
[1] 249958      3
 > x[1:10,]
        P3-real.CEL   P4-real.CEL  P5-real.CEL
 [1,]  1.001874e-23 -2.117582e-22 4.567573e-08
 [2,]  1.603000e+03  1.240000e+03 2.319708e-39
 [3,] -8.589935e+09  1.454000e+02 2.759000e+03
 [4,]  3.503246e-44  8.100000e+01 4.539706e-08
 [5,]  5.238000e+02  4.010000e+02 2.319436e-39

 > result.degradation<- AffyRNAdeg(result.batch)
Error in var(x, na.rm = na.rm) : missing observations in cov/cor
In addition: There were 50 or more warnings (use warnings() to see the 
first 50)
 >
 > MAplot (result.batch)
Error in rowQ(imat, half) : cannot handle missing values  -- yet
In addition: Warning message:
NaNs produced in: log(x, base)