Negative Value On Linear Gene Expression In Microarrays

Question

[fbrundu]

Hi all, I am starting to use microarrays and maybe this is a dumb question:

Using Illumina microarrays, linear gene expression can be negative? Or maybe some artefacts have been introduced?

And, in this case, how to correct them? With scaling (adding the absolute value of the minimum negative value) or flooring (converting negative values to zeros)?

Thanks

Answer 1

[Sean Davis]

This may result from background subtraction. To my knowledge, there is not a standard approach to dealing with this situation, but the two approaches you point out are not uncommon.