log transform
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8/10/2019 Log Transform
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Description: Apply a log transformation on a GCT file.
Author: Dr Mark Cowley (Garvan Institute of Medical Research, SydneyAustralia), [email protected]
Kevin Ying (Garvan Institute of Medical Research, SydneyAustralia), [email protected]
Date: September, 2011
Release: 3.3
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Apply a log base 2 transformation to data from a GCT file.
Why? Typically microarray data are log transformed. This is done for a number ofreasons, including: it stabilizes the variance; it compresses the range of data; and itmakes the data more normally distributed, which allows statistics to be applied to thedata.
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Why do some microarray data have negative values anyway?
Its usually because of background subtraction. If a gene is expression close to, or justbelow the background level on the array, then these data may become negative. This iscertainly true is you use the IlluminaExpressionFileCreator, with the backgroundsubtraction mode = true, and is true for Agilent microRNA data.
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To apply the strategies described above:
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To help you decide how to handle values
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