I can read soft files in R using GEOquery. They are normalized, but we can't always tell how. Most of the times it's not in log. Can I normalize this data using other methods? Actually I normalize .CEL easily in R, but this dataset just has Soft and txt file. I need to normalize soft file using method in log? Is there any possible way to do this for example with RMA?

I used following command, but unfortunately the output file contains a lot of NA and -inf?

Is there any way to normalize GEO data in soft format?

> library( GEOquery )
> geo <- getGEO( "GDS3513" )
> geo
> eset = GDS2eSet(geo, do.log2 = TRUE)

File stored at: 
C:\Users\Fariba\AppData\Local\Temp\Rtmp0slTe9/GPL4133.annot.gz
There were 32 warnings (use warnings() to see them)

> write.exprs(eset,file="C:\\Users\\Fariba\\Desktop\\data.txt")