[BioC] problems with gcrma just.gcrma

[Elisabetta Manduchi]

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.

> 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.
>