User: avelarbio46

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avelarbio4610
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Posts by avelarbio46

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Comment: C: WGCNA - networking RNA seq gives only one module!
... After some reading, I've been trying some other normalization techniques. As per WGCNA basis, I've done log2(x+1), which radically changed my results (more clusters and power treshold got to over 0.9 within 7 power) and PCA dimension 1 lowered to 17 variance. Do you have any advices on scaling? Log ...
written 6 months ago by avelarbio4610
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Comment: C: WGCNA - networking RNA seq gives only one module!
... Any techniques to test for spurious expressions drivers? My PCA seemed good, with Dim 1 representing 66% of data variation and Dim 2 6%, which was good for how much data I used.I have tested VAT graphs on distance matrices and they seem pretty good also, indicating nice clustering. Also I'm startin ...
written 6 months ago by avelarbio4610
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Comment: C: WGCNA - networking RNA seq gives only one module!
... Indeed, using all genes at once changed it a bit, but not too much as the turquoise block is still big. It is very strange to find a big cluster which is not expected for the disease I'm studying, but might be very helpful also! One thing is that I'm working with one tissue, so maybe the turquoise ...
written 6 months ago by avelarbio4610
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WGCNA - networking RNA seq gives only one module!
... Hello everyone! I'm doing WGCNA co-expression analysis on 29 samples related to a specific disease, with RNA-seq data with 100million reads. After all quality control, I ended up with 53000 genes in FPM measure. I then filtered all genes with 0 variance, miRNA and pseudogenes, also genes that had l ...
network wgcna R co-expression written 6 months ago by avelarbio4610 • updated 6 months ago by Peter Langfelder2.3k

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