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All images were background corrected setting the signal outside the hyphae to zero to obtain a sufficiently dark background.
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Raw feature intensities were background corrected using the RMA background correction algorithm [ 21, 22].
The raw data were background corrected by subtracting the background median from the foreground median intensity for both red and green intensities; negative results were set to 1.
The signal was background corrected using the normexp method [ 62].
Specifically, images were background corrected using the background subtraction function with a rolling ball radius of 50 pixels.
The mean intensity is taken for each spot and background corrected by subtracting the surrounding median local background intensity.
First, we background corrected the data using NOOB [ 47].
Figure 2b is a QQ plot of the background corrected PM intensities (on the original scale) versus quantiles from an exponential distribution for the same data set.
The background corrected intensities were averaged across the six TT hybridization data sets.
The enrichment of ChIP DNA over input DNA was calculated as ratio of the background corrected ChIP signal divided by the background corrected input signal (both globally normalised).
Gene expression values were background corrected and normalized globally using the default setting of the Affymetrix Microarray Suite 5.0 software, and log2-transformed according to the Affymetrix Statistical Algorithm Reference Guide (Affymetrix, Inc. 2004b).
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