Different Values Between Affymetrix Power Tools And Affy R Package

Question

[lkmklsmn]

Hi, I needed to convert a bunch of CEL files into an expression matrix.I did this in two different ways: 1) using Affymetrix Power Tools and 2) Affy R package. Both times I used the rma method. The values in the expression matrices are not exactly the same.They are generally pretty close but not the same.

e.g.

3.91778  2.70814  5.16966  4.73077
3.92947  2.72072  5.21682  4.78799

Why not?

Answer 1

[Neilfws]

Short answer is that you'd have to compare the code for APT and affy/rma to figure out what's causing the difference. It might be something as simple as using different numbers of significant figures in the calculation. As you note, the differences are minor and they're unlikely to impact downstream analysis very much.

[Irsan]

Yup, I agree. It us unlikely that the values are exactly the same. There should be high correlation between the 2 though. You can calculate the Pearson correlation between the 2 and make a scatterplot