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

[James W. MacDonald]

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
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099