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Always Log
Always log spot intensities and ratios Why? Because it Comments: Logs base 2 are the easiest for people (intensities are typically a number between 0 to 65535). In a context
like this, a single standard deviation (SD) can be given the usual
interpretation only if
Compare the histograms for unlogged and logged intensities and ratios (Figure 1). Figure 1 Variation of log intensities is still not constant: a noticeable decrease as magnitude increases remains evident in most microarray data (Figure 2). When we have two sets of numbers such as R and G varying over a large range, it is useful to compare log R with log G by plotting their difference log(R/G) against their average (1/2)log R*G. Doing this we might see something unexpected. By contrast, plotting R against G is typically much less revealing and can give a quite unrealistic sense of concordance (Figure 2). Figure 2
Further comments. As noted above,
log ratios still have a spread which tends to decrease as average log intensity
increases. This suggests that a different transformation of the ratio might
achieve a more constant scatter (at least as a function of average log
intensity). This is indeed the case: a ratio of 4th or 5th roots does
seem to have a more constant scatter (about 1). However, we feel this is
a small gain compared to the simplicity (adding/subtraction logs corresponding
to multiplying/dividing) lost if logs are not used. For example, normalization
is no longer straightforward. We will stick with logs until a more compelling
reason comes along.
last updated March 07, 2000
