constructing a reference matrix from affy 2.0 chip for a 4.0 chip.

Question

[RNAseqer]

I have some expression for isolated immune cell subsets. I want to use these to make a reference matrix deconvolution. However, this work was done on Affymetrix Multispecies miRNA-1 Array my work was done on miRNA4.0 chips. The expression data is listed on GEO as series GSE28489. Its given identifiers are probe set IDs (ex. hsa-miR-181a-2-star_st). determining the corresponding expression values in my data to pull out for a comparison to the reference matrix I have constructed from this is giving me some trouble.

Is there a ready conversion tool available to help me determine what values I should take from my data to compare to these values from a Affymetrix U133 Plus 2.0 chip? Are the probe set ID#s for these versions of the chip comparable? If so is there a ready tool I could use to convert the 2.0 probe set Ids into ID#s?

How would you go about pulling the corresponding information from a 4.0 chips RMA log2 normalized data?

[Kevin Blighe]

I am not sure whether or not it helps, but you may take the second approach that I mention here:

• A: How to integrate multiple data sets from microarray platform prior meta-analysis