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

Wed Mar 19 11:59:19 CET 2014

Dear Amit,

Package xps is available for R-3.0.2:
http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/xps_1.22.2.zip 

However, since you are using Windows you need to install a special 
version of ROOT, which is compiled with MinGW. Currently you can 
download this ROOT version from:
https://docs.google.com/file/d/0B0qZ3XBoK1ubVzl5MHBEaWxQdW8/edit

Alternatively, I could send you this version (37 MB).
Please read the README file how to install ROOT and xps for Windows.

Regarding the custom array GPL5928 (for Plasmodium falciparum) that you 
are using:
In order to use xps, you would need not only the CDF-file 
'GPL5928_scrMalariaa.CDF' but also at least the probe sequences in 
tabular format 'GPL5928_scrMalariaa.probe.tab' (which you can normally 
download from Affymetrix together with the CDF-file).

Best regards,
Christian

On 3/19/14 6:18 AM, amit kumar subudhi wrote:
> 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 at aon.at
> <mailto:cstrato at 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 <http://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 at gmail.com <mailto:amit4help at gmail.com>
> amit.subudhi at pilani.bits-pilani.ac.in
> <mailto:amit.subudhi at pilani.bits-pilani.ac.in>
> Mob No- 919983525845
>