Question: Suggestion To Change Cuffdiff -C "Min Alignment Count" Default To Author'S Value Of '10'
0
Kevin Silverstein • 20 wrote:
Hi Galaxy Developers,
This is regarding the wrapper for cuffdiff and the -c parameter for
"Min
alignment count". We noted that Galaxy's default value is set to
1000. In
our experience, setting this parameter that high yields drastically
different results from the ones obtained with the author's original
default
value of c = 10.
The -c parameter is defined as:
-c/--min-alignment-count <int> The minimum number of alignments in a
locus
for needed to conduct significance testing on changes in that locus
observed
between samples. If no testing is performed, changes in the locus are
deemed
not signficant, and the locus' observed changes don't contribute to
correction for multiple testing. The default is 10 fragment
alignments.
We have found that the value entered will require that at least this
number
of fragment alignments be found for *each* sample (or at least each
condition) in order for the locus to be tested for differential
expression.
Although one could save themselves a lot of locus comparisons (and
hence
take a much smaller hit for multiple hypothesis testing) if he/she
were to
raise this threshold, this will screen out the most desirable
differentially
expressed genes - specifically those that are not expressed at all in
one
condition but highly expressed in the other condition.
The attached image has a real example of a gene that was counted as
differentially expressed (as it should have been) with '10' but was
not even
tested at '100' nor '1000'.
-Kevin Silverstein
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modified 6.6 years ago
by
Jeremy Goecks • 2.2k
•
written
6.6 years ago by
Kevin Silverstein • 20
