Hello Jim and Christian,

Jim, I am extremely sorry for not providing all the information that are
needed for diagnosing the problem. The array that I am using is a custom
made Affy array with GEO Platform ID GPL 5928. As I have mentioned earlier,
the array hybridization data is in public through GEO and is a work of a
separate group. What I can get information from the published literature is
that, this array is seems like a PM only array and is* not a *3' biased
array.

below is the details of the commands used, errors and sessionInfo

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)

sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United
States.1252

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
base

other attached packages:
[1] scrmalariaacdf_1.37.0 AnnotationDbi_1.22.6  BiocInstaller_1.10.4
 limma_3.16.8          affy_1.38.1
[6] Biobase_2.20.1        BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] affyio_1.28.0         DBI_0.2-7             IRanges_1.18.4
 preprocessCore_1.22.0 RSQLite_0.11.4
[6] stats4_3.0.2          tools_3.0.2           zlibbioc_1.6.0

*Now I have tried to download the xps package to use the dabg.call command
to compute the P/M/A calls but it is returning the information as 'xps' is
not available (for R version 3.0.2).*

source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.12 (BiocInstaller 1.10.4), ?biocLite for help
A newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
> biocLite("xps")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.2.
Installing package(s) 'xps'

   package 'xps' is available as a source package but not as a binary

Old packages: 'e1071', 'Rcpp'
Update all/some/none? [a/s/n]:
a
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.0/e1071_1.6-3.zip'
Content type 'application/zip' length 800125 bytes (781 Kb)
opened URL
downloaded 781 Kb

trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.0/Rcpp_0.11.1.zip'
Content type 'application/zip' length 3009433 bytes (2.9 Mb)
opened URL
downloaded 2.9 Mb

package 'e1071' successfully unpacked and MD5 sums checked
package 'Rcpp' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Amit\AppData\Local\Temp\RtmpM7Omit\downloaded_packages
Warning messages:
1: *package 'xps' is not available (for R version 3.0.2)*
2: installed directory not writable, cannot update packages 'boot',
'cluster', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv',
  'nlme', 'rpart', 'survival'

*Should I install a older R version to use the XPS? Please also let me know
if I need to give any other information. *

Regards
Amit


On Tue, Mar 18, 2014 at 7:59 PM, cstrato <cstrato@aon.at> wrote:

> 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,
> Christian
> _._._._._._._._._._._._._._._._._._
> 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
>>>
>>>
>>


-- 
Amit Kumar Subudhi
Research Scholar,
CSIR-Senior Research Fellow,
Molecular Parasitology and Systems Biology Lab,
Department of Biological Sciences ,
FD III, BITS, Pilani,
Rajasthan- 333031
e mail-
amit4help@gmail.com
amit.subudhi@pilani.bits-pilani.ac.in
Mob No- 919983525845

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