Question: Limma import array layout GenePix files
0
gravatar for Guillaume Robert
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?

Thanks for your help

microarray limma layout • 175 views
ADD COMMENTlink modified 8 months ago by Gordon Smyth38k • written 8 months ago by Guillaume Robert0
Answer: Limma import array layout GenePix files
2
gravatar for Gordon Smyth
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.

ADD COMMENTlink modified 8 months ago • written 8 months ago by Gordon Smyth38k

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

ADD REPLYlink written 8 months ago by Guillaume Robert0
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