[BioC] Reading MAGE-ML cdf into bioconductor for limma in R v. 3.0.2

Ben Temperton [guest] guest at bioconductor.org
Mon Mar 31 09:43:55 CEST 2014

Hi there,

I am trying to load some microarray data from ArrayExpress into R for analysis with Limma:


However, the probe set needs to be installed first for this to work, and the probe set is in MAGEML format. Previously, I've only ever dealt with the makecdfenv package that uses .cdf files. I found a package called RMAGEML in bioconductor that looked like it would do the job, but it is not available with R v. 3.0.2.

I was hoping you might have some insight into how best to approach this problem.

Many thanks,

 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-redhat-linux-gnu (64-bit)

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ArrayExpress_1.22.0 Biobase_2.22.0      BiocGenerics_0.8.0  R.utils_1.29.8      R.oo_1.18.0         R.methodsS3_1.6.1  

loaded via a namespace (and not attached):
[1] affy_1.40.0           affyio_1.30.0         BiocInstaller_1.12.0  limma_3.18.13         preprocessCore_1.24.0
[6] tools_3.0.2           XML_3.98-1.1          zlibbioc_1.8.0

Sent via the guest posting facility at bioconductor.org.

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