TiMAT2 results typically include:


File/ Directory Index:

Trm Trimmed mean relative difference window score
Pse Pseudo median relative difference window score
Sum Wilcoxon rank sum window score, -10Log10(p-value) transformed
QVal Multiple test corrected symmetric p-value estimation of trm or pse window scores, -10Log10(q-value) transformed
RndPVal Random label permutation based uncorrected p-value using either the trm or pse window scores, -10Log10(p-value) transformed
RndFDR Random label permutation based FDR using either the trm or pse window scores, -10Log10(FDR) transformed
Win Directory containing serialized Window[]s for downstream TiMAT2 application use.
Oligo Individual aveT/ aveC oligo ratios, log2 transformed, score assigned to the center position of the oligo.
HM Heat map or stair step
sgr.zip SGR file format for direct viewing in IGB, text, tab delimited, chromosome position score.
gr.zip GR file format for viewing in IGB, be sure to select the appropriate chromosome in IGB prior to loading a gr file. Tab delimited, position score.
bar binary file format for viewing in IGB. See the Bar2Gr to convert to txt.
bed Tab delimited chrom, start, stop coordinates for the intervals
xls Excel spreadsheet containing a variety of statistics for each interval, tab delimited text.