The detection algorithm uses probe pair (includes perfect-match (PM) and mismatch (MM)) intensities to generate a detection p-value and assign a Present, Marginal, or Absent call.
Finally, a median polishing algorithm is used to summarize the background-corrected, normalized probe intensities to generate a final probe set value.
Finally, a median polishing algorithm was used to summarize the background-corrected and the normalized probe intensities to generate a final probe set value.
The detection algorithm uses probe pair intensities to generate a detection p-value and assign a "present", "marginal", or "absent" call.
Gene-level summarization algorithms, which combine multiple probe intensities to generate an overall expression estimate for the gene, can suffer from biases of probe cross-hybridization.
The median background intensity was subtracted from the median spot intensity to generate the background-corrected signal intensity for use in further analysis.
The motor threshold will be found in the region of the cortex with the least intensity necessary to generate a peripheral response.
Foreground (signal) and background intensities were generated separately for Cy3 and Cy5 channels, and the local background intensity was subtracted to generate a corrected intensity for each spot.
The band intensity was quantified to generate a standard curve connecting signal strength and protein amount.
FastUnifrac (Hamady et al, in review [24]) with branch length weighting by taxon relative abundance (normalized log-transformed fluorescence intensity) was used to generate a phylogenetic distance matrix from the PhyloChip data.
