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Blanking (i.e. background) was performed on monolayers stained only with second antibody and reacted as above.
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Background subtraction was performed on-line.
However, at BC3F3 stage, marker-assisted background analysis was performed on multiple QTL-near-isogenic lines (NILs) selected for maximum phenotypic similarity with the RP.
RMA background adjustment was performed on each chip.
Background normalization was performed on raw methylation data according to Marabita et al. [ 53].
The same rolling ball background subtraction was performed on each image.
As recommended in the VSN manual, no background correction was performed on the Affymetrix probe intensities prior to VSN-normalization.
By default, all non-control probe sets were used as a background, and analysis was performed on the aspect of "biological process" using the hypergeometric test.
In early generations of backcrossing, the background selection for RPG recovery was performed on the basis of morphological similarity of the backcross-derived lines with the RP (Singh et al. 2015).
A paired-samples t-test was performed on background EMG levels (% MVC) recorded during the two tasks, TD and ND.
More details on sample preparation is given in previous descriptions of this experiment [ 29] and the data is available in GEO [ 45] with the accession number GSE53170 [ 46]. Background correction and quantile normalisation was performed on the microarray data (GSE53170) using the R package LIMMA [ 47] from Bioconductor [ 48].
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