Question: find significant analysis?
1
gravatar for star
12 months ago by
star140
Netherlands
star140 wrote:

I have done Differential expression (DE) analysis and found 2212 DE genes in my data, then I found the overlap between my DE genes and some diseases related genes (e.g. ALS). ALS disease contains 1007 genes that 500 of those had overlap with DE genes. Now I would like to find these number are significant or not?

statistic fisher.test R • 245 views
ADD COMMENTlink modified 12 months ago by Rasoul Godini0 • written 12 months ago by star140
3
gravatar for arta
12 months ago by
arta540
Sweden
arta540 wrote:

You can use hypergeometric test which is similar to fisher test and in the following link you can find an example about how to do that.

ADD COMMENTlink written 12 months ago by arta540

There is also an R package especially for this purpose, geneOverlap.

ADD REPLYlink written 12 months ago by Benn6.6k
0
gravatar for Rasoul Godini
12 months ago by
Rasoul Godini0 wrote:

Hi To find significancy you need an statistical threshold like p-value. to make that you need some repeats. But in here you have only genes selected by a threshold already. Here, you can use Venn diagram to show common DEGs and punctuate on findings by writing about percentage of your DEGs which are common with disease specific genes. Good Luck

ADD COMMENTlink written 12 months ago by Rasoul Godini0
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