Use of TPM cutoff for Affymetrix GeneChip Genome Arrays

Question

[libelletje]

Hello everyone,

I have question related to the use of a TPM cutoff for Genome Array data. I am using the PyWGCNA approach to extract gene modules. However, this algorithm was intended to be used for RNA-seq data, as such, for the filtering of lowly expressed genes, it used a TPM cutoff. I have selected a value that allows me to retrieve my ideal number of modules. However, as this was intended for RNA-seq data and I am using genome array measured data, is there any possible implication in the extraction of my conclucions or is it interchangable because they have been both normalized and are associated with expression level?

Thank you in advance!