[BioC] mas5calls with make.cdf.env

[Lana Schaffer]

Jim,
GCOS is making the mas5calls with these CDF files.
Lana 

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Thursday, June 07, 2007 11:20 AM
To: Lana Schaffer
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] mas5calls with make.cdf.env

Looks to me like you might have a PM-only chip. Is this the case?

Best,

Jim

Lana Schaffer wrote:
> 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
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>Search the archives: 
>>http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 
> 
> --
> 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
> 
> 
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should 
> not be used for urgent or sensitive issues.


--
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


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not
be used for urgent or sensitive issues.