Question: Enrichment analysis for class comparison
gravatar for Bnf83
23 months ago by
Bnf83130 wrote:

Hi Guys, sorry if the question might sound stupid but I'm not sure about how to set a statistical test. Basically I have 2000 breast cancer patients that had surgery. Of them, 1000 had additional tumours (not secondary but primary tumours) divided according to the following classes.

Class A      50
Class B      250
Class C      450
Class D      250

Total: 1000

The 1000 patients are further divided in pre-post surgery as follows:

Class A       20
Class B      150
Class C      120
Class D       75

Class A       30
Class B      100
Class C      330
Class D      175

Now I would like to compare the dataset PRE with the dataset ADDITIONAL in order to see if there's some enrichment as well as the dataset POST with the dataset ADDITIONAL for the same reason. I already have compared the PRE-POST between them. I suppose I have to perform a Fisher test but I' m a little bit confused on how to write the contingency table. Can anyone help me please?

Thank you in advance

Best regards


fisher R • 458 views
ADD COMMENTlink modified 23 months ago by WouterDeCoster39k • written 23 months ago by Bnf83130

I think you should change your post from Job to Question

ADD REPLYlink written 23 months ago by Medhat8.3k

I just did that ;-)

ADD REPLYlink written 23 months ago by WouterDeCoster39k


column PRE + column POST = column ADDITIONAL

So, I am unsure whether it makes sense to compare one PRE or POST column to the margin column.

My two cents.

ADD REPLYlink modified 23 months ago • written 23 months ago by SamGG20

Hi, if I well understand you are showing only half of the data. You said that you have 2000 patients. So 1000 are in the ADDITIONAL group and 1000 are in another group NO_ADDITIONAL. For the NO_ADDITIONAL you should create again the PRE and POST tables and compare them. Also, it would help if you further detail what kind of enrichment are you looking for. Enrichment in categories of PRE compared to POST or enrichment in categories of PRE in ADDITIONAL compared to PRE in NO_ADDITIONAL?

ADD REPLYlink written 23 months ago by Fabio Marroni2.2k
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