Hello,

I am currently working on gene co-expression network (GCN) analysis, specifically focusing on the inference and analysis of GCNs using R. I have generated a SummarizedExperiment object using an RPKM expression matrix, a GTF file for gene annotation, and associated sample metadata. However, I am uncertain whether the processing steps were correctly implemented.

To verify the consistency of my processed expression matrices (final_exp1 and final_exp2), I used the following comparison:

identical(
    assay(final_exp1)[1:5, 1:5],
    assay(final_exp2)[1:5, 1:5]
)

This returned FALSE, indicating a discrepancy between the two matrices, despite both having the same dimensions. I am unsure what may have caused this difference.

Additionally, I attempted to perform functional enrichment analysis using the module_enrichment() function with MapMan annotations:

sea_mapman <- module_enrichment(
    net = gcn,
    background_genes = rownames(final_exp1),
    annotation = gma_annotation$MapMan
)

However, the analysis did not return any enriched terms. I am uncertain whether this is due to an issue with the annotation object, the network structure, or the format of background genes.

Could you please advise me on:

Possible reasons for the discrepancy between final_exp1 and final_exp2, even when dimensions match.

How to ensure that module_enrichment() works correctly with MapMan annotations, and what checks I should perform on the inputs.

Thank you in advance for your guidance.

Best regards, Sabina Tiwari