[BioC] appropriate statistical test for post-array analysis

[Naomi Altman]

"location shift" is the difference in medians.

--Naomi

At 02:00 PM 8/17/2007, r.athanasiadou wrote:
>Hi everyone,
>I have used Nimblegen oligo arrays for ChIP-chip experiments.
>
>I now have my results of which genomic regions are getting enriched in my
>experiment.
>
>I have calculated some values like GC-content of all the sequences on the
>array and I would like to test if the distributions of these values remain
>unchanged in the group of enriched sequences.
>
>My intuition was the wilcoxon (Mann-Whitney) test but after discussing with
>a colleague I really don t know if this is the best approach.
>
>Additionally, if Wilcox.test is the correct approach, do I need to
>pre-process the data? ie should I just put in the function the raw values of
>every probe or should I first group them and put the frequencies for each
>value in the function? I tried both approaches and they produce opposite
>results.
>
>I am worried that when I feed the raw values, there is a bias to accept the
>alternative hypothesis because of the huge difference in the actual number
>of values in the two groups.
>
>
>Could anyone point me to the correct statistical direction?
>
>Finaly,what does the "location shift" that the Wilcox.test output refers to
>mean? Is it the difference of medians?
>
>Thank you
>Niki
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111