Co-expression gene network

Question

[Mohita]

Hello All,

I want to build Co-expression network for GEO dataset (microarray / RNA seq). for this I am trying CEMiTool. I have studied the paper and then i tried CEMiTool by using example file gievn in the tutorial. But when I am trying for my dataset I could not able to get the result. my question is for CEMiTool we need to give only expression file as input or we have to make some changes in dataset file (GSE series matrix.txt). I am new to this field so i could not understand the many things. Please help me to resolve the Problem. I will be very greatful.

Thanks and Regards Mohita

Answer 1

[pedrostrusso]

Hi Mohita!

For CEMiTool, you must provide a data.frame containing expression data with genes in rows and samples in columns, as can be seen from the image below, taken from the webCEMiTool website:

So more directly, yes, you'll need to adjust your data to get it into this format.