Y-axis is # of element reported on a certain genome that has been scrambled. X - axis is the size of the sliding window within which this random shuffling was performed. The assumption made here by the author, and I am advancing that notion, (not sure if it is entirely correct or not, nevertheless) that when I discover elements on a scrambled genome, it has to be, by definition, a false positive

Conversely, the elements that I discover and report on the original, unshuffled genome, have to be, by definition, true positives

Just the comparison of original Vs unscrambled genomes in terms of # of elements reported in each case, was used by the software author to report FDR. FDR = (# element in shuffled genome) / (# elements in original genome) * 100 (in %)

My chart does NOT show the # of elements in the original genome without any DNA random shuffling. Those numbers are as follows:

A. thaliana (original genome, no DNA shuffle) - 885 elements

B. rapa (original genome, no DNA shuffle) - 3686 elements

M. truncatula (original genome, no DNA shuffle) - 1808 elements

As expected, these numbers above, for the unshelled genomic DNA as input, yields higher # of elements than for the same genomes that have undergone random DNA shuffling (irrespective of what the sliding window size is. So at least in this context, I am seeing what is 'expected' in terms of the shuffled genome serving as a negative control, and yielding fewer # of elements than for randomly shuffled genomes.

In reply to Re^6: Window size for shuffling DNA? by onlyIDleft
in thread Window size for shuffling DNA? by onlyIDleft

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.