[BioC] Make cdf package error Human Exon array

[James W. MacDonald]

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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> 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
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099