[BioC] problems with gcrma just.gcrma

James W. MacDonald jmacdon at med.umich.edu
Tue Dec 5 17:53:11 CET 2006


Hi Elisabetta,

Elisabetta Manduchi wrote:
> 
> Jim,
> 
>> Hi Elisabetta,
>>
>> I see your problem now. First, you are using just.gcrma() rather than 
>> justGCRMA(), which is the function you should be using. The problem 
>> here is that you are passing an argument 'samepleNames' to 
>> just.gcrma() which a.) doesn't exist for this function, and b.) is 
>> misspelled.
>>
>> Even if you had been using justGCRMA(), you would have errored out in 
>> the same manner because the misspelled argument will be passed to the 
>> function incorrectly. We will have to fix that problem. However, if 
>> you use justGCRMA() with sampleNames = sample.names, it should work 
>> for you.
> 
> 
> good eyes, thanks! I didn't notice the mispelling. I guess I'm used to R
> complaining when one passes in a non-existing argument name.

The 'problem' with the justRMA() and justGCRMA() functions is that the 
first argument is '...', which is there to allow one to do justGCRMA() 
and automagically use all celfiles in the working directory. The 
downside of this is that any malformed argument will be grabbed up by 
the '...' argument and added to the filenames, which is what was 
happening in your case. This also precludes an error message for a 
non-existing argument name because the '...' argument allows any 
argument to be passed in.

I'll be fixing this in the next couple of days and pushing the fix to 
the release repository.

Best,

Jim


> 
>> NB; you can still use list.celfiles() if you want to use a subset of 
>> the chips. You can always subset using the '[' function (i.e., 
>> list.celfiles()[1:4]). However, you would probably have to use the 
>> celfile.path argument as well, since list.celfiles() won't give you 
>> the path information. Using filenames = 
>> list.celfiles("../../data_repository/quantifications")[some subset], 
>> celfile.path = ("../../data_repository/quantifications") is probably 
>> easier than typing out all the celfiles with their path information.
> 
> 
> Yes, I was aware of subsetting and passing a celfile path, but it 
> appeared to be about the same amount of work as just listing the full 
> filenames of interest.
> 
> Thanks again!
> Elisabetta
> 
>>
>> Elisabetta Manduchi wrote:
>>
>>>
>>> Hi Jim,
>>> thanks for your feedback. They appear to be all .CEL files:
>>>
>>>> cel.files
>>>
>>>
>>>  [1] 
>>> "../../data_repository/quantifications/NDminus_E15.5_Pan_11-13-03_MGU74Av2.CEL" 
>>>  [2] 
>>> "../../data_repository/quantifications/NDminus_E18_Pan_MGU74Av2.CEL"
>>>  [3] "../../data_repository/quantifications/NDminus_P1_Pan_MGU74Av2.CEL"
>>>  [4] 
>>> "../../data_repository/quantifications/NDminus_P1_PanIslet_MGU74Av2_3-4-03.CEL" 
>>>  [5] 
>>> "../../data_repository/quantifications/CGC_NDmutant_John_Sample_4_MGU74Av2.CEL" 
>>>  [6] 
>>> "../../data_repository/quantifications/NDplus_E15.5_Pan_11-13-03_MGU74Av2.CEL" 
>>>  [7] 
>>> "../../data_repository/quantifications/NDplus_E18_Pan_MGU74Av2rescan.CEL" 
>>>
>>>  [8] "../../data_repository/quantifications/NDplus_P1_Pan_MGU74Av2.CEL"
>>>  [9] 
>>> "../../data_repository/quantifications/NDplus_P1_PanIslet_MGU74Av2_3-4-03.CEL" 
>>> [10] 
>>> "../../data_repository/quantifications/CGC_Wild_John_Sample_3_MGU74Av2.CEL" 
>>>
>>>
>>>>
>>>
>>> I've checked them one by one and they are indeed .CEL. I didn't use 
>>> list.celfiles because I'm only using a subset of the .CEL files 
>>> contained in this directory.
>>> Elisabetta
>>>
>>> ---
>>>
>>> On Mon, 4 Dec 2006, James W. MacDonald wrote:
>>>
>>>> Hi Elisabetta,
>>>>
>>>> Elisabetta Manduchi wrote:
>>>>
>>>>> Hello,
>>>>> I'm trying to use just.gcrma with data from Affy MGU74Av2 and am 
>>>>> getting the error at the bottom of what's copied below re 
>>>>> read.probematrix. I'm running version 2.4.0 of R and gcrma version 
>>>>> 2.6.0. The mgu74av2 packages being downloaded are version 1.14.0.
>>>>> Can anybody advice on what I can do to overcome this?
>>>>
>>>>
>>>>
>>>> That error usually means that you are not pointing to celfiles with 
>>>> your filenames argument. What do you get if you type
>>>>
>>>> cel.files
>>>>
>>>> at the R prompt? It is often easier to use filenames=list.celfiles().
>>>>
>>>> Best,
>>>>
>>>> Jim
>>>>
>>>>
>>>>> Thanks,
>>>>> Elisabetta
>>>>> ---
>>>>>
>>>>>> data.gcrma<-just.gcrma(filenames=cel.files, type=c("fullmodel"), 
>>>>>> normalize=T, optimize.by=c("memory"), fast=T, 
>>>>>> samepleNames=sample.names)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Computing affinities[1] "Checking to see if your internet 
>>>>> connection works..."
>>>>> trying URL 
>>>>> 'http://bioconductor.org/packages/1.9/data/annotation/bin/windows/contrib/2.4/mgu74av2cdf_1.14.0.zip' 
>>>>> Content type 'application/zip' length 1340750 bytes
>>>>> opened URL
>>>>> downloaded 1309Kb
>>>>>
>>>>> package 'mgu74av2cdf' successfully unpacked and MD5 sums checked
>>>>>
>>>>> The downloaded packages are in
>>>>>          C:\Documents and Settings\Elisabetta Manduchi\Local 
>>>>> Settings\Temp\Rtmpc7v1qb\downloaded_packages
>>>>> updating HTML package descriptions
>>>>> [1] "Checking to see if your internet connection works..."
>>>>> trying URL 
>>>>> 'http://bioconductor.org/packages/1.9/data/annotation/bin/windows/contrib/2.4/mgu74av2probe_1.14.0.zip' 
>>>>> Content type 'application/zip' length 2396326 bytes
>>>>> opened URL
>>>>> downloaded 2340Kb
>>>>>
>>>>> package 'mgu74av2probe' successfully unpacked and MD5 sums checked
>>>>>
>>>>> The downloaded packages are in
>>>>>          C:\Documents and Settings\Elisabetta Manduchi\Local 
>>>>> Settings\Temp\Rtmpc7v1qb\downloaded_packages
>>>>> updating HTML package descriptions
>>>>> .Done.
>>>>> Error in read.probematrix(filenames = filenames, which = "pm", 
>>>>> cdfname = cdfname) :
>>>>>          VECTOR_ELT() can only be applied to a 'list', not a 'symbol'
>>>>> ---
>>>>>
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>>>>
>>>>
>>>>
>>>>
>>>> -- 
>>>> James W. MacDonald
>>>> University of Michigan
>>>> Affymetrix and cDNA Microarray Core
>>>> 1500 E Medical Center Drive
>>>> 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.



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