About negative correlation...

[inscara]

Hi,

Is there anyway to get the list of genes that are negatively correlated with the query gene?

Thanks in advance and regards,

inscara.-

[Andrew Su]

Hello,

There is no easy way to search for negative correlations through the
web interface. However, you can download the raw data from our
downloads page and do the correlation analysis on single genes in
excel without too much difficulty.

As an aside, we consciously focused on positive correlation
coefficients through BioGPS. We've looked into the question of
negative values in the past, but couldn't find any evidence of
significant and biologically meaningful results.

Cheers,
-andrew

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[inscara]

Hi Andrew,

Thanks for the reply. I've downloaded the
geneatlas_MOE430_20090327.raw.avg.csv.zip raw data file.
Could you explain me how to use those raw values? Are they intensity
values? Should I normalize them
or do something else before use those values for correlation?

Thanks in advance and regards,

Cesar.-

[Andrew Su]

Hi Cesar,

Those values are normalized intensity values using gcrma. Unless you
have a specific reason to normalize differently, the values as shown
reflect a good general-purpose normalization.

Cheers,
-andrew