[BioC] Make cdf package error Human Exon array

[James W. MacDonald]

Hi Maria,

A quick glance at the PREDA vignette indicates to me that you can use 
already processed data. See e.g., page 7-8 of the PREDAtutorial, and 
?statisticsForPREDAfromEset.

Best,

Jim



On 4/4/2013 1:20 PM, Maria Arnedo Munoz wrote:
> Hi Jim!
>
> The problem is that I really need to build a cdf environment in order 
> to analyse these arrays with the PREDA package and when I look for it 
> in the bioconductor website I can't find it because it isn't there.
>
> I am trying to compare the gene expression between two different cell 
> lines but not focus in specific genes, I like to know if there are 
> huge (or big enough) chromosome regions with different gene expression 
> between the two cell lines (the PREDA package makes this kind of 
> analyses), and the only array that I have found for both is a HuEx.
>
> So, does anyone know how to do that? If it isn't possible I will try 
> to analyse with another package that makes the same kind of analyses.
>
> Thank you
>
> Best
>
> Maria
>
> Quoting "James W. MacDonald" <jmacdon at uw.edu> on Thu, 04 Apr 2013 
> 11:56:58 -0400:
>
>> Hi Maria,
>>
>> On 4/4/2013 11:44 AM, Maria [guest] wrote:
>>> Hello everybody!
>>>
>>> I am not sure if this is the way for asking because I am new in this 
>>> kind of "help-website" so, please if I am wrong tell me.
>>
>> You asked your question perfectly! Nice work.
>>
>>>
>>> I am trying to make a cdf package for the Human Exon Array chip from 
>>> Affymetrix (HuEx-1_0-st-v2). I have downloaded the file 
>>> HuEx-10-st-v2.cdf from the Affymetrix website and write the 
>>> following commands in the R program:
>>>
>>> library(makecdfenv)
>>> pkgpath<-tempdir()
>>> make.cdf.package("HuEx-1_0-st-v2.text.cdf",cdf.path="/Working/HuEx-1_0-st-v2.r2",compress=F, 
>>> species = "Homo_sapiens", package.path = pkgpath)
>>>
>>> It costs me a lot of time and most of the RAM memory of my computer 
>>> and at the end the following message appears:
>>>
>>> Reading CDF file.
>>> Error in .Call("reaD file", as.character(file), as.integer(3),
>>> as.integer(compress), :promise already under evaluation: recursive 
>>> default
>>> argument reference or earlier problems?
>>>
>>> I have no idea if I am doing anything wrong or if there is a better 
>>> method for making the package, so any help will be really welcome.
>>
>> You are doing something wrong - the makecdfenv package isn't designed 
>> for these types of arrays, which is why it failed. To analyze exon 
>> arrays, you have two choices. You can either use the oligo or xps 
>> package. I am unfamiliar with xps, but Christian Stratowa, the author 
>> of that package is very helpful.
>>
>> I am more familiar with oligo. For this package you can just load the 
>> package and then do something like
>>
>> dat <- read.celfiles(list.celfiles())
>>
>> assuming you started R in the same directory that contains your 
>> celfiles. Otherwise you need to add in path information so these 
>> functions can find the files. You can then do
>>
>> eset <- rma(dat)
>>
>> and depending on the goals of your analysis, you can select the level 
>> at which you want to summarize your data. See ?rma for more information.
>>
>> Best,
>>
>> Jim
>>
>>
>>>
>>> Thank you,
>>>
>>> Maria
>>>
>>>  -- output of sessionInfo():
>>>
>>> R version 2.15.3 (2013-03-01)
>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_United Kingdom.1252
>>> [2] LC_CTYPE=English_United Kingdom.1252
>>> [3] LC_MONETARY=English_United Kingdom.1252
>>> [4] LC_NUMERIC=C
>>> [5] LC_TIME=English_United Kingdom.1252
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] makecdfenv_1.36.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affy_1.36.1           affyio_1.26.0         Biobase_2.18.0
>>> [4] BiocGenerics_0.4.0    BiocInstaller_1.8.3   preprocessCore_1.20.0
>>> [7] zlibbioc_1.4.0
>>>
>>> -- 
>>> Sent via the guest posting facility at bioconductor.org.
>>>
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>>
>> -- 
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>>
>>
>>
>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099