How to change values in a dataframe Python

I think simpliest is use replace by dict:

np.random.seed(100)
df = pd.DataFrame(np.random.choice(['n','y','?'], size=(5,5)), 
                                   columns=list('ABCDE'))
print (df)
   A  B  C  D  E
0  n  n  n  ?  ?
1  n  ?  y  ?  ?
2  ?  ?  y  n  n
3  n  n  ?  n  y
4  y  ?  ?  n  n

d = {'n':0,'y':1,'?':1}
df = df.replace(d)
print (df)
   A  B  C  D  E
0  0  0  0  1  1
1  0  1  1  1  1
2  1  1  1  0  0
3  0  0  1  0  1
4  1  1  1  0  0

This should work:

for col in df.columns():
   df.loc[df[col] == 'n', col] = 0
   df.loc[df[col] == 'y', col] = 1
   df.loc[df[col] == '?', col] = 1