Extract the genes of each group pattern

[elcega]

Can you extract as a data.frame a list of the genes included on each of the groups generated
after degPlotCluster(res3$normalized, "condition") ?

[lpantano]

this function is only a proxy for plotting, so res3$normalized contains all the information you are seeing. Normally the column cluster has the group number you see in the plot, and you should have a column for genes, and the scaled expression as well. let me know if you don't find them.

[elcega]

Hey Lorena, yes, you are right, I see the cluster column. q) Just to confirm, is the "value" column defining which genes are most variable across x-axis "times"? Maybe is here but I have missed it https://bioconductor.org/packages/release/bioc/manuals/DEGreport/man/DEGreport.pdf

And so, from my understanding, the number of clusters is done based on a cut off (0.001-0.98) and a minimum number of genes per group. I have read you mentioned this cutoff can be defined in some kind of benchmarking function, but I have not seen any examples. Do you have any reproducible examples of using different cutoffs? I would like to try these different cut-offs to see how many groups and genes fall into these.