deisygysi / wto Goto Github PK

Hi,

I want to use wTO and CoDiNA to compare the co-expression networks of M. endlicherianum (an alga) under different growth (stress) conditions. In total, we have 38 different growth conditions, and for each condition, we have three biological replicates. I was wondering whether there is a minimum number of samples to build a network via wTO or not.
For example, the WGCNA authors suggested building networks with at least 20 samples. I wanted to build one network for similar stress conditions, however, I do not know what is the minimum number of suggested samples in this algorithm. Is it similar to WGCNA, i.e. do I have to put at least 7 conditions together (7 conditions * 3 replicates each)?

Best regards,
Armin Dadras

Hi,

I am trying to use your package on a bunch of datasets on a powerful computer (265 CPU and 2T RAM) and I have around 14000 genes after filtering and cleaning my datasets. At the beginning, I was using wTO.Complete to build my networks. And I got this error:

Error in data.table::rbindlist(OUTPUT, idcol = idcol) : Total rows in the list is 2721559750 which is larger than the maximum number of rows, currently 2147483647

I noticed it is related to the memory limits in R (source).
However, the other function wTO.fast does not have this problem and I can build my networks with it. I noticed that in the wTO.Complete there is line that is implemented (omitted?) differently in wTO.fast.

Since wTO.Complete provides more information to investigate the quality of the network, is it possible for you to modify this part of its code so it works on large datasets too?

Best regards,
Armin