Hello,

I finally ran maSigPro and Would like to save final results of DE genes in data.frame format. I also would like to extract the genes that are in the same cluster. how can I do that ?

Thanks in advance

Simon

hello simon,

i gues that it is a little bit late but i want to help if i can.

for the clusters i use:

<cluster=see.genes(get$sig.genes,k=9)

<write.table(cluster$cut, file = "output_cluster")

together with:
<write.table(get$sig.genes$sig.profiles, file = "output_sig.profiles")
<write.table(get$sig.genes$sig.pvalues, file = "output_sig.pvalues")

it is easy to look at the data in excel.

So, I got to this discussion/question recently, although this is from more than 5 years ago. Anyway, would someone knows how to plot individual graphs from the different cluster generated?

Currently, I'm running the following code:

see.genes(get_groups$sig.genes$XffvsMock, show.fit = T, dis =AX_design$dis,
                cluster.method="hclust", cluster.data = 1, k = 9)

From that, I'm getting, obviously, 9 graphs, but, unfortunately, grouped all together. I would like to see each graph separately. Right now I can't see the legends of each graph, because they are kind of overlapping each other, which is making them all really lame and not useful for presentation or publication.

This is an example of the overlapped plots:

This is an example from maSigPro paper which is also what would like to get: