svndigest - svndigest

Rev	Date	Author	Line
2	26 Feb 07	jari	1	<html>
2	26 Feb 07	jari	2	<body bgcolor = "#FFFFCC"><basefont face = "Arial">
2	26 Feb 07	jari	3	<h1>Data Adjustment: Lower Cutoffs</h1><h2>Parameter Information</h2>
2	26 Feb 07	jari	4	<hr size = 10>
2	26 Feb 07	jari	5
2	26 Feb 07	jari	6	<h2>Overview of Lower Cutoffs</h2>
2	26 Feb 07	jari	7	The lower cutoff data adjustment is used to trim out genes having low intensity
2	26 Feb 07	jari	8	data. The trim criteria is such that if any one expression value for a gene falls
2	26 Feb 07	jari	9	below the Cy3 or Cy5 intensity value cutoffs then that gene will excluded from
2	26 Feb 07	jari	10	further analysis. This method is rather stringent since the entire gene is removed
2	26 Feb 07	jari	11	from analysis if it fails for one intensity in one experiment.
2	26 Feb 07	jari	12	<br><br>
2	26 Feb 07	jari	13	One possible utility is to exclude genes with missing data by setting the
2	26 Feb 07	jari	14	cutoffs to a very low value such as 1. The possibility of exclusion increases
2	26 Feb 07	jari	15	with increased number of experiments making this feature impractical for many
2	26 Feb 07	jari	16	data sets.<br><br>
2	26 Feb 07	jari	17	Note that if the goal is to make sure that a gene has valid data representing
2	26 Feb 07	jari	18	most of the experiments, percentage cutoffs is a more flexible alternative.
2	26 Feb 07	jari	19	<br>
2	26 Feb 07	jari	20	</basefont>
2	26 Feb 07	jari	21	</body>
2	26 Feb 07	jari	22	</html>