I was trying to calculate t-statistics using Python's
numpy as np-
scipy.stats.ttest_ind_from_stats( NP.mean(x[['GSM1224991', 'GSM1224992']]), NP.std(x[['GSM1224991', 'GSM1224992']]), len(['GSM1224991', 'GSM1224992']), NP.mean(x[['GSM1224993', 'GSM1224994']]), NP.std(x[['GSM1224993', 'GSM1224994']]), len(['GSM1224993', 'GSM1224994']), )
For example in the dataset given below,
GSM1224991 & GSM1224992 are in first group and
GSM1224993 & GSM1224994 form second group.
Here is the calculation given in GEO2R analysis for the same reference but while I calculate t test it is
0.029630766122806237 instead of
-0.33768 something as shown below.
ID adj.P.Val P.Value t B logFC 148000 1 0.001426 -9.44 -0.33768 -2.513
How to calculate t-stat here? Or considering single row is wrong approach?