An average microarray signal intensity > 20 was used as cut off.
molecular weight cut off.
Scanning and data analyses were performed as previously described, with a signal cut-off intensity of 100 to remove low-intensity/poorly hybridized spots from the analysis.
The data sets were filtered using a signal cut-off intensity of 100 to remove low-intensity/poorly hybridized spots from the analysis.
Features such as secondary structure, melting temperature, and even target characteristics make it difficult to define a cut-off intensity for gene presence [ 11, 12].
Otsu's early and still commonly used approach (Otsu, 1975) picks a cut-off intensity based on the gray-value histogram of an image, considering pixel intensities below this threshold as background and pixels exceeding the threshold intensity as foreground.
Briefly, masking for both Cy5 (HPL) and DAPI (Nuclei) channels was generated by setting the mask dimensions and cut-off intensity above the background for each of the two channels and intensities were quantified in the area covered by the masking.
The S. coelicolor transcripts were divided into three abundance classes using the following intensity cut-offs: Intensity < 2000 as rare, 2000 < Intensity < 20000 as intermediate and >20000 as abundant sequences.
To optimize the Splitter intensity threshold parameter for the Agilent platform, we conducted a series of analyses over a range of log ratio cut-off intensities from 2.25 to 2.75 standard deviations of the distribution, with and without prior application of normalization, to the Whitehead dataset.
The raw intensity cut off value of 80 was determined based on the base over proportional (C = a/b) calculation, which is generated by plotting the standard deviation of normalized values against the control values.
