[BioC] Problem with mas5calls, bugs?

[Lizhe Xu]

After using the rma, I used mas5calls to read the flag call from Affy U133A .txt file. But I was surprised to find that the mas5calls got quite different results compared to the original .txt file (798 inconsistance for 22283 probe sets for a group of 6 arrays, when comparing with the DMT). Is it something I did wrong or a bug for this command?
Here is what I did: 

> library(affy)
Welcome to Bioconductor 
         Vignettes contain introductory material.  To view, 
         simply type: openVignette() 
         For details on reading vignettes, see
         the openVignette help page.

Synching your local package management information ...
> Data<-ReadAffy()
> pData(Data)
                      sample
9 1 337a.CEL       1
9 2 395a.CEL       2
9 3 396a.CEL       3
4 1 338a.CEL      4
4 2 342a.CEL      5
4 3 341a.CEL      6

> rmaData<-rma(Data)
Background correcting
Normalizing
Calculating Expression

> Dataf<-mas5calls(Data)
22283 ids to be processed
.........
> pData(Dataf)
                      sample
9 1 337a.CEL       1
9 2 395a.CEL       2
9 3 396a.CEL       3
4 1 338a.CEL      4
4 2 342a.CEL      5
4 3 341a.CEL      6

> gn<-geneNames(Dataf)

> gn[5870]
[1] "206344_at"
> gn[7686]
[1] "208180_s_at"

> exprs(Dataf)[5870,]
 C:/Program Files/R/rw1081/9 1 337a.CEL  C:/Program Files/R/rw1081/9 2 395a.CEL 
                                            "A"                                             "P" 
 C:/Program Files/R/rw1081/9 3 396a.CEL C:/Program Files/R/rw1081/4 1 338a.CEL 
                                            "A"                                             "P" 
C:/Program Files/R/rw1081/4 2 342a.CEL C:/Program Files/R/rw1081/4 3 341a.CEL 
                                            "M"                                             "A" 
> exprs(Dataf)[7686,]
 C:/Program Files/R/rw1081/9 1 337a.CEL  C:/Program Files/R/rw1081/9 2 395a.CEL 
                                            "M"                                             "A" 
 C:/Program Files/R/rw1081/9 3 396a.CEL C:/Program Files/R/rw1081/4 1 338a.CEL 
                                            "A"                                             "P" 
C:/Program Files/R/rw1081/4 2 342a.CEL C:/Program Files/R/rw1081/4 3 341a.CEL 
                                            "M"                                             "A" 

Here I took two probeset as example (out of 798): for 206344 in the original .txt file the flags are A, P, A, "A", M, A
for 208180 in the original .txt file the flags are "P", A, A, P, "P", A

Thanks.


Lizhe