[BioC] Error message after mass5calls command MAS5.0 absolute detection

cstrato cstrato at aon.at
Tue Mar 18 15:29:19 CET 2014

Dear Amit,

As Jim did already mention, mas5calls do work only for arrays containing 
PM/MM-oligos. For PM-only arrays Affymetrix has developed an alternative 
to mas5calls, which is called DABG calls.

As Jim kindly said, package xps has implemented function dabg.call() for 
PM-only arrays. However, function mas5.call() is implemented in xps in a 
way that does also work for PM-only arrays, although I would recommend 
to use dabg.call().

Best regards,
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

On 3/18/14 3:16 PM, James W. MacDonald wrote:
> Hi Amit,
> On 3/18/2014 2:54 AM, amit kumar subudhi wrote:
>> Hello,
>> I am trying to get the A/P calls from a Affybatch file but getting the
>> below errors.
>> # read the .cell file from the working directory
>> Data= ReadAffy()
>> To run the AP call algorithm used the command on the AffyBatch file
>> Data = mas5calls(Data)
>> #The following message is appearing
>> PAcalls= mas5calls(Data)
>> Getting probe level data...
>> Computing p-values
>> Error in FUN(1:43[[1L]], ...) :
>>    NA/NaN/Inf in foreign function call (arg 2)
>> Can anybody let me know where could be the problem is?
> Probably, but you don't give near enough information, particularly what
> kind of arrays you are using. If I were to hazard a guess I would bet
> that you are using a PM-only array, in which case there is no way to
> compute the conventional mas5calls (because without MM probes the
> conventional P/A/M calls can't be computed).
> IIRC, there is a way to compute something similar, implemented in the
> xps package, for the PM-only arrays. But Christian Stratowa would be the
> one to say for sure.
> And if you are using 3'-biased arrays, please let us know what array,
> and the output from sessionInfo().
> Best,
> Jim
>> Regards
>> Amit

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