[BioC] mas5calls with make.cdf.env

[James W. MacDonald]

Lana Schaffer wrote:
> Jim,
> GCOS is making the mas5calls with these CDF files.

I'm confused. Does that mean it is or is not a PM-only chip?


> 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.


-- 
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.