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Question: WGCNA: Matching eigengenes to samples
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gravatar for Jack
12 days ago by
Jack0
Jack0 wrote:

When using WGCNA it would be useful to match eigengene values to the corresponding sample IDs, but I can't seem to find a way to do this. 

Taken from the tutorial (part I.2a.), blockwiseModules takes a data expression file (datExpr), with sample IDs:

net = blockwiseModules(datExpr, power = 6,
                     TOMType = "unsigned", minModuleSize = 30,
                     reassignThreshold = 0, mergeCutHeight = 0.25,
                     numericLabels = TRUE, pamRespectsDendro = FALSE,
                     saveTOMs = TRUE,
                     saveTOMFileBase = "femaleMouseTOM",

verbose = 3)

Within net, you then have the dataframe MEs, which contains the modules in the columns and has a number of rows equal to the number of samples imported, but they are unlabelled. I suspect these represent the samples in the order they were imported, but I am not sure. Does anyone know if this is the case, or if it is possible to generate a table containing the eigengene values and sample names?

Hope someone can help!

Jack

 

 

ADD COMMENTlink written 12 days ago by Jack0

Yes, you are right. The MEs data frame contains module (columns) Eigen values for each sample (rows). Just label row names of MEs with the sample names of your input expression data matrix.

ADD REPLYlink modified 11 days ago • written 11 days ago by vijay.muley0
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