Question: Limma import array layout GenePix files
0
8 months ago by
France/Nantes/Inovarion
Guillaume Robert0 wrote:

Hi everyone,

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?

microarray limma layout • 175 views
modified 8 months ago by Gordon Smyth38k • written 8 months ago by Guillaume Robert0
Answer: Limma import array layout GenePix files
2
8 months ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

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.