[BioC] Make cdf package error Human Exon array

[Maria Arnedo Munoz]

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
>
>
>



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