I am very new to R and gene expression Analysis, so i hope my question does not sound that silly
So I am trying to reproduce the results of a certain Series from the GEO database. According to their paper they normalized the data in expression level of a certain housekeeping gene.
I have the .cel files and created a phenodata file, with the name, filename and target information and saved the data with the function readaffy in a variable. So i am not sure how to normalize the data in respect to the housekeeping gene in R. (i know how to do it in excel, but could not find an option to open the cel files in excel).
Another question is: they used the ddCT method to calculate the fold induction value, but to recalculate it with this method I would need the Ct , am I right? Is there a way to get it through the raw dat (.cel files)?
Thank you very much!