How to set a cell to NaN in a pandas dataframe

just use replace:

In [106]:
df.replace('N/A',np.NaN)

Out[106]:
    x    y
0  10   12
1  50   11
2  18  NaN
3  32   13
4  47   15
5  20  NaN

What you’re trying is called chain indexing: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy

You can use loc to ensure you operate on the original dF:

In [108]:
df.loc[df['y'] == 'N/A','y'] = np.nan
df

Out[108]:
    x    y
0  10   12
1  50   11
2  18  NaN
3  32   13
4  47   15
5  20  NaN