Entering edit mode
15 months ago
Ronin
▴
10
Hi all,
I've got a couple of questions about my output from getDifferentialPeaks.pl in Homer. I have compared two eye samples from different conditions. I am posting a portion of the output file below:
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| #PeakID chr start end strand score focus ratio/other Total Tags Background Tags Fold Change vs. Background p-value | |
| VHII01000037.1-56 VHII01000037.1 2086 3306 + 858.9 1220 1588 177.6 8.94 0.00e+00 | |
| VHII01000031.1-40 VHII01000031.1 132534 133200 + 669.3 666 1225.5 75.7 16.19 0.00e+00 | |
| VHII01000031.1-26 VHII01000031.1 129642 130013 + 196.8 371 361 29.1 12.4 5.54e-253 | |
| VHII01000031.1-72 VHII01000031.1 138309 138683 + 148.8 374 269.5 12.1 22.22 7.97e-253 | |
| VHII01000037.1-79 VHII01000037.1 1445 1780 + 143.2 335 322 1 331.87 0.00e+00 | |
| CM020915.1-2292 CM020915.1 41485917 41486515 + 135.2 598 250.5 25.2 9.93 1.11e-153 | |
| VHII01000037.1-182 VHII01000037.1 112451 112695 + 130.8 244 236.5 19.4 12.19 2.87e-164 |
My first question is: How is the focus ratio and score actually calculated -- that is, what exactly is it saying?
And my second question: When I have large focus ratio, but a p-value reading 00e+00, does this mean the p-value is simply too small to be recorded accurately, or that this is actually not a statistically significant peak?
Thank you in advance,
