Question: All Adjusted P values in GEO2R are equal to 1?
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gravatar for jabbari.parnian
4 weeks ago by
jabbari.parnian0 wrote:

Hi everyone,

I have tried the GEO2R tool for different datasets on GEO, with different groupings. But I'm surprised that all my adjusted P values are either equal to 1 or 0.998. Does anyone have any idea why this happens?

Thanks

microarray geo2r geo • 100 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by jabbari.parnian0

Probably because there is no difference between the groups. Can you compare it to the work published using this dataset? How many replicates did you have and how does the grouping looks like? You might need to export the data to have a deeper look (try PCA for instance)

ADD REPLYlink written 4 weeks ago by Asaf8.3k

@asaf It would be very strange that all datasets run into the same problem. And I have compared some of the datasets with the work they published, the authors had found DEGs, but I don't get them with GEO2R with the same grouping.

ADD REPLYlink written 4 weeks ago by jabbari.parnian0

Yes, that's indeed weird. Can you share such an example?

ADD REPLYlink written 4 weeks ago by Asaf8.3k

I have tried GSE83300 and GSE143222. with different groupings. But all result in adjusted p values of 1.

ADD REPLYlink written 4 weeks ago by jabbari.parnian0

GSE83300 is all glioblastoma tissues and GSE143222 all breast cancer tissue, how would you group them to compare one group against the other? Usually it will be done by comparing tumor vs. normal or other comparison like this.

ADD REPLYlink written 4 weeks ago by Asaf8.3k

In the article based on GSE143222 they have compared those with complete response and those with non-complete response, for example.

ADD REPLYlink written 4 weeks ago by jabbari.parnian0

I compared recurrence with non recurrence samples and got low p-values (0.0996) using the default parameters (just clicked top 250)

ADD REPLYlink written 4 weeks ago by Asaf8.3k
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