It seems that when comparing two Series objects, index is ignored, here is an trivial example

In [177]: pd.show_versions()

INSTALLED VERSIONS
------------------
commit: None
python: 2.7.7.final.0
python-bits: 64
OS: Linux
OS-release: 3.2.0-0.bpo.4-amd64
machine: x86_64
processor:
byteorder: little
LC_ALL: None
LANG: en_US

pandas: 0.14.0
nose: 1.3.0
Cython: 0.19.2
numpy: 1.8.1
scipy: 0.14.0
statsmodels: 0.5.0
IPython: 2.0.0
sphinx: 1.1.3
patsy: 0.2.1
scikits.timeseries: None
dateutil: 1.5
pytz: 2014.3
bottleneck: None
tables: 3.0.0
numexpr: 2.2.2
matplotlib: 1.3.1
openpyxl: 1.6.2
xlrd: 0.9.2
xlwt: 0.7.5
xlsxwriter: None
lxml: 3.2.3
bs4: 4.3.1
html5lib: None
bq: None
apiclient: None
rpy2: None
sqlalchemy: 0.8.3
pymysql: None
psycopg2: None


In [158]: a = pd.Series([100, 101, 102, 103], index=[1,2,3,4])
In [168]: b = pd.Series([102, 103, 104, 105], index=[3, 4, 5, 6])

In [170]: a
Out[170]:
1    100
2    101
3    102
4    103
dtype: int64

In [171]: b
Out[171]:
3    102
4    103
5    104
6    105
dtype: int64

In [172]: a > b
Out[172]:
1    False
2    False
3    False
4    False
dtype: bool

In [173]: a < b
Out[173]:
1    True
2    True
3    True
4    True
dtype: bool

In [174]: a == b
Out[174]:
1    False
2    False
3    False
4    False
dtype: bool

In [175]: a - b
Out[175]:
1   NaN
2   NaN
3     0
4     0
5   NaN
6   NaN
dtype: float64

Comment From: jreback

see discussion here: https://github.com/pydata/pandas/issues/1134

This is a feature!

Comment From: longislandfarmer

Thanks for the link, can this be documented/highlighted in documentation? It's really not obvious!

Comment From: jorisvandenbossche

@jreback you say it is a feature, but we discussed it in the issue you referenced, and you also had a PR https://github.com/pydata/pandas/pull/6860 that had the intention to change this?

Comment From: jreback

@jorisvandenbossche I know, but I don't think its easy to change this, so can't happen in 0.15.0 maybe later. let's just document for now.

@mjnicky want to take a stab at this?

Comment From: jorisvandenbossche

This was fixed in https://github.com/pandas-dev/pandas/pull/13894 for 0.19.0