I'm currently analyzing a public microarray dataset (https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-104/)
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