I am trying to export module eigengene values, calculated using 'Tutorial I.2a. Automatic network construction and module detection'.

I can extract the MEs using:

MEs = net$MEs

Which contains the information I need - MEs per subject (sample). However, the sample identification is lost, and replaced with numbered values. How can I tie these results back to the original sample information? Are these simply listed in the same order as the originally imported samples?

Thank you.

The simplest way to do it, assuming your expression data carry valid rownames:

rownames(MEs) = rownames(datExpr)

(replace datExpr with the object that carries our expression data).

More generally, you can add a column to MEs that has sample ID, or multiple columns that have all the information you need, from the datTraits data frame (calculated in Section 1 of the tutorial).

HTH,

Peter