Limma import array layout GenePix files
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Last seen 2.5 years ago

Hi everyone,

I'm currently analyzing a public microarray dataset (

I've managed to import the GenePix files into limma thank to the commands :

cols = list(R  = "GenePix:F635 Mean",    G  = "GenePix:F532 Mean", Rb = "GenePix:B635 Median", Gb = "GenePix:B532 Median")
RG_array1 = read.maimages(targets, annotation="Reporter identifier", columns=cols)

I am now at the within-array normalization step, and I understand that I need the array layout informations if I want to perform a print-tip loess normalization.

This layout have not been imported in my RGlist object when I used the function read.maiages. I've found out that those layout information can be in a ".gal" file, but I don't think this file is present on the public repository. However informations about positions (blocks, row and columns) are indeed present in the .gpr files.

I was wondering if it is possible to import layout information into a RGlist object without a .gal file, from the positions informations present in the .gpr file?

Thanks for your help

limma microarray layout • 425 views
Entering edit mode
Last seen 9 hours ago
WEHI, Melbourne, Australia

To do print-tip normalization, you only need to know the layout of the arrays. In your case, this would be

layout <- list(ngrid.r=12, ngrid.c=4, nspot.r=26, nspot.c=26)
MA <- normalizeWithinArrays(RG_array1, layout=layout, method="printtiploess")

Alternatively, rather than specify the layout to normalizeWithinArrays, you can store it in the RGList itself by

RG_array1$printer <- layout

I learned the layout just by looking at one of the gpr files. The layout entries are just the maximum values taken by the columns metaRow, metaColumn, row and column respectively.

Entering edit mode

It's working fine! Thank you again for your precious help.


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