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Interpretation of combined P values - RNA microarray meta analysis

I am currently trying to do a microarray / RNA seq meta analysis with the DExMA package in R.

meta_ultra_common_genes <- metaAnalysisDE(
  objectMA = NULL,
  effectS = NULL,
  pvalues = meta_p_common_list,
  weight = NULL,
  typeMethod = "maxP",
  missAllow = 0.3,
  proportionData = 0.5) 

 head(meta_common_genes)
             Stat         Pval          FDR     AveFC propDataset
NPSR1-AS1 0.35949596 2.158560e-03 3.790594e-02 0.5953627           1
SLCO1B3   0.58023185 3.816009e-02 2.240394e-01 1.0155570           1
SERPINB3  0.73673204 1.599033e-01 4.682648e-01 0.6532639           1
SERPINB7  0.60229642 4.773772e-02 2.533574e-01 0.7801785           1
OLFM4     0.06590374 8.193329e-08 2.481948e-05 1.6880326           1
SERPINB4  0.92666729 6.332030e-01 8.678512e-01 0.4086473           1

when using e.g. the combined p value method max p it shows the max. p value under "Stat". What I don't understand is why the "Pval" or the "FDR" are ways lower in the results object.

Can you help me interpret this?

metaanalysis r microarray dexma combinedp
• 931 views • link
written by hagl • hagl

1 answer

Hey, Why do you think the Stat represents the p-value? As far as I know, Stat represents the test statistic, FDR is p-val*numer_of_rows

• 0 views • link
written by chemokine-1 • chemokine-1

Thank you for the reply. I know that "Stat" displays the maximum p value of each row (maxP "calculation") because I compared it to my data and calculated the maximum p values manually. What I don't understand is why the p_val and the FDR are lower than the max p

• 0 views • link
written by hagl • hagl

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