[BioC] mas5calls with make.cdf.env

[Lana Schaffer]

James,
>sessionInfo() 
R version 2.5.0 (2007-04-23) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"
"datasets" 
[7] "methods"   "base"     

other attached packages:
makecdfenv       affy     affyio    Biobase 
  "1.14.0"   "1.14.0"    "1.4.0"   "1.14.0" 

> traceback()
7: .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, x]), 
       as.character(pns), as.integer(length(mms[, x])), as.double(tau), 
       as.double(sat), dpval = double(length(unique.pns)),
length(unique.pns), 
       PACKAGE = "affy")
6: FUN(1:6[[1L]], ...)
5: lapply(X, FUN, ...)
4: sapply(1:length(pms[1, ]), function(x) {
       .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, 
           x]), as.character(pns), as.integer(length(mms[, x])), 
           as.double(tau), as.double(sat), dpval =
double(length(unique.pns)), 
           length(unique.pns), PACKAGE = "affy")$dpval
   })
3: mas5calls.AffyBatch(object, ...)
2: mas5calls(abatch)
1: mas5calls(abatch)

Thanks,
Lana




-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Thursday, June 07, 2007 6:19 AM
To: Lana Schaffer
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] mas5calls with make.cdf.env

Hi Lana,

Lana Schaffer wrote:
> Hi James,
> R version 2.5.0 (2007-04-23)
> makecdfenv   "1.14.0"
> I am following the vignette for makecdfenv to create a new cdfenv and 
> can use this env for functions llike plotHist but I get an error when 
> using the function mas5calls.
> Error: 
> Getting probe level data...
> Computing p-values
> Error in FUN(1:6[[1L]], ...) : NA/NaN/Inf in foreign function call 
> (arg
> 2)
> This is my code:
> mycdfenv <- make.cdf.env("myname.CDF") abatch <- ReadAffy() 
> abatch at cdfName <- "mycdfenv"
> Calls <-mas5calls(abatch)
> -Error-
> Can someone help me get the mas5calls function to work here?

How about giving us a sessionInfo() and a traceback() after the error.

Best,

Jim


> Thanks,
> 
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu
> 
> _______________________________________________
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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