[BioC] average difference and global scaling for normalizing affymetrix expression data?

[Alice Johnstone]

Hello,

I have been asked to look at data from the GEO to make a comparison with current microarray data.  The GEO data is from an Affymetrix Murine Genome U74 Version 2 Array experiment, from 2003 and the description says that the data is the "average difference" with "global scaling" applied.

This means there are negative values for some probesets and the values range from -831.8 to 12785, but the majority sit around 15-300.

My question is what is the best way to proceed?  Do I take this as normalized data?  A boxplot of the data shows some variation between the samples.  Should I just remove the negative values and then proceed with limma with log2 of the data.  
Or will I need to make further transformations before I apply the linear model?  if so, which?
Im wary of over manipulating the data as its only a 2x2 comparison to begin with.

Thanks for your advice.
Alice
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