Question: Integrating Samples into a Single Dataset
0
gravatar for Parisa
4.0 years ago by
Parisa0
United States
Parisa0 wrote:

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. 

ADD COMMENTlink modified 4.0 years ago by cpad011212k • written 4.0 years ago by Parisa0
0
gravatar for cpad0112
4.0 years ago by
cpad011212k
India
cpad011212k wrote:

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?

ADD COMMENTlink written 4.0 years ago by cpad011212k

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.

ADD REPLYlink written 4.0 years ago by Parisa0

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 u would have a normalized input file ready to upload in GRN inference tools or package like minet package for CLR gene regulatory network inference

ADD REPLYlink written 3.9 years ago by Angel3.5k
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