Log-transformation by default?

[Chun Shen Lim]

Hi,

First of all thank you for maintaining the user friendly platform. I did microarray analysis using the default settings: PreprocessDataset -> ExpressionFileCreator -> ComparativeMarkerSelection.

Have the mean values of the final output (.odf) being log-transformed by default?

Cheers,

Chun Shen

[Edwin Juarez]

Hello Chun Shen,

I am glad that you find GenePattern useful!

By default, ComparativeMarkerSelection does not log-transform your data, you would need to change the "log2 transform" parameter in that module to change that.

Here is a link to the documentation if you want to take a closer look: http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/PreprocessDataset/6

Let me know if that helps!

Edwin.