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gevaertlab / MethylMix

Identification of differentially methylated genes in biomedical data
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how to add batches to matrix? #5

Open ahwanpandey opened 4 years ago

ahwanpandey commented 4 years ago

Hello,

METcancer = matrix(data = methylation_data, nrow = nb_of_genes, ncol = nb_of_samples)
METnormal = matrix(data = methylation_data, nrow = nb_of_genes, ncol = nb_of_samples)
GEcancer = matrix(data = expression_data, nrow = nb_of_genes, ncol = nb_of_samples)
ClusterProbes(MET_Cancer, MET_Normal, CorThreshold = 0.4)

If the data contains batches, the user must provide numeric batch data within the matrices. MethylMix can be applied on all illumina arrays, including the newly released Epic platform and any array that outputs beta values. At the moment there are no restrictions to input sequencing-based methylation data, if the data is formatted in proportions however, as mixture modeling is computationally expensive, Methylmix will require more time to finish.

I don't understand this part. Can you explain how I am supposed to put the batch information into the matrix? Do you mean add a new row like this?

image

Thanks.

ahwanpandey commented 4 years ago

Hi just wondering if you had the chance to look into this?

Thanks.