[BioC] ArrayExpress as NChannelSet data into limma-compatible type

Chris Fjell cfjell at interchange.ubc.ca
Wed Sep 23 01:02:35 CEST 2009

I've been trying with no success to analyze 2-channel array data from
ArrayExpress. The scanner specific data files are not available (I've
used ImaGene files previously with ease.)

I used the ArrayExpress package to get the data very conveniently and
easily. The data are loaded into R as NChannelSet data.

I cannot sort out how to get this into a format acceptable by limma.
It's easy enough to access the channels as well as annotations but limma
methods such as (for example) limma's normalizeWithinArrays()

     normalizeWithinArrays(object, layout, method="printtiploess",
weights=object$weights, span=0.3, iterations=4, controlspots=NULL, df=5,
robust="M", bc.method="subtract", offset=0)


     object: object of class 'list', 'RGList' or 'MAList' containing red
          and green intensities constituting two-color microarray data.

> ae = ArrayExpress("E-FPMI-11", rawcol=list(R="Software Unknown:Signal
Mean_cy5", G="Software Unknown:Signal Mean_cy3", Rb="Software
Unknown:Background Mean_cy5", Gb="Software Unknown:Background Mean_cy3"));
> class( ae )
[1] "NChannelSet"
[1] "Biobase"
> test = normalizeWithinArrays( ae )
Error in MA.RG(object, bc.method = bc.method, offset = offset) :
  Object doesn't contain R and G components

I also notice that the convert routines will convert to NChannelSet but
not from NChannelSet to other types such as used by limma (RGList, MAList).

I am tempted to now write the data back to file and construct a generic
2-color data object using limma::read.maimages(). But this seems an odd
thing to do.

I've also tried getting the data directly to file and then using the
RMAGEML package but it seems to not install due to need for SJava
installed which won't install on either Mac (my workstation) or Linux
Ubuntu 7.10 due to compilation errors in the SJava C code (subject of
another post if needed).

How do I use NChannelSet data or convert to RGList or MAList?

Thanks for any help...

Christopher Fjell, PhD
Centre for Microbial Diseases and Immunity Research
Department of Microbiology and Immunology
University of British Columbia
2259 Lower Mall
Vancouver, British Columbia, Canada, V6T 1Z4

cfjell at interchange.ubc.ca / chris at cmdr.ubc.ca

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