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about P-value

about P-value
2009.06.24. 11:38
 I have a few questions about the Wilcoxon rank sum test in this software.
1. How does Wicoxon test identify the major bins of genes? Does it use Log fold-change of my uploading data?
2. If the p-value of the Wilcoxon rank sum test is more than 0.05, that will mean the BIN function would not be true. Is that right?

Re: about P-value
2009.06.26. 10:04 válaszként erre: Dear yw.
The Wilcoxon test:

You can imagine it to be conceptually similar to a t-test, however it uses ranks instead of the underlying data and thus doesn't need (approximate) normality of data.

It then tests if the changes within a BIN are more extreme than the changes in all the remaining genes. However, as said before this is done on a rank scale.

An example:
BIN 1, 3 genes with log2 FC
gene 1 -2
gene2 -3
gene3 -0.5

all other bins 4 genes
geneA 1
geneB 0.2
geneC -0.2
geneD 2

ranks BIN1
gene1 2
gene2 1
gene3 3

ranks rest
geneA 6
geneB 5
geneC 4
geneD 7

A t-test would evaluate this as barely significant p=0.046, whereas the Wilcox test would not detect any significant change (p=0.057).

Please note that like always the failure to detect a significant change doesn't necessarily imply that there is no change.