Hi, Can I continue the analysis after obtening the toptable of differentially expressed genes using the R code of GEO2R or I should do my own analysis? I have many samples in my dataset, how can I define the groups in GEO2R because it influence the result of the toptable. The normalization in GEO2R is the Log transformation ?? Thank you in advance
GEO2R is just an interface between R and the Gene Expression Omnibus (GEO) database. It usually allows you to directly import data that is already normalised. The normalisation type, if Affymetrix microarray data, will most likely consist of a 3-step process known as RMA (Robust Multiarray Average) normalisation:
- background correction
- quantile normalisation
- log base 2 transformation
When you import this data into R, you can do anything that you want with it. Usually people fit a linear model with limma and then extract the statistical representations of this model via the
If you wish to merge datasets ('groups'?) together, then they should ideally be from the same microarray version.
Further questions, ask away.