Integrating Samples into a Single Dataset

Question

[Parisa]

Hi,

I have a few sample files from series GSE 12982 and GSE 5334. All of them are .CEL files. I am trying to make a simple GRN with this data. I need to integrate samples into a single data set before I can apply the CLR algorithm. I wonder if anybody here can help me to make that single data set from all the data I have.

Thank you

Answer 1

[cpad0112]

They are from two different experiments. One is cell line based and the other one, animal model based. I am not sure if it is a good idea to combine, even after normalization. Can you not apply CLR independently (to each data set) and then compare GRN?

[Parisa]

I probably need to try what you are saying. I started with these two series, but at the end, I need to use much more experiments and find the regulatory relationships that are specific to cell and tissue types of common developmental origins. That's why I was thinking of having everything in a single dataset.

[zizigolu]

Parisa,

I think you could install Robina simply on windows, then upload your CEL files in, see if you could grouping them, means assign each CEL to a similar groups. I think by reading few page of microarray part of robina manual you could figure out. Then you would have a normalized input file ready to upload in GRN inference tools or package like minet package for CLR gene regulatory network inference