Negative expression values on Affy array
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Laura
Oct 10, 2011, 1:12:56 PM10/10/11
to dChip Software
Hi,
I have questions about how to use (and perhaps whether to use)
negative expression values resulting from normalization using dchip.
The experimental data I am looking at was run on the Affymetrix Human
Genome U133 Plus 2.0 Array, and the dchip normalized expression values
are available as GSE8977 (NCBI GEO). For some spots on the array, all
samples have negative values, and for some other spots, maybe 2-4 (or
less, or more) of the values are negative. I am new to micro array
analysis, and particularly single channel arrays, and I am wondering
if there is a standard way to handle these kinds of values. Should I
assume there is essentially no expression at these spots, or should I
use cel files and re-normalize the data? Use absolute calls? Please
advise. Many thanks in advance.
I have questions about how to use (and perhaps whether to use)
negative expression values resulting from normalization using dchip.
The experimental data I am looking at was run on the Affymetrix Human
Genome U133 Plus 2.0 Array, and the dchip normalized expression values
are available as GSE8977 (NCBI GEO). For some spots on the array, all
samples have negative values, and for some other spots, maybe 2-4 (or
less, or more) of the values are negative. I am new to micro array
analysis, and particularly single channel arrays, and I am wondering
if there is a standard way to handle these kinds of values. Should I
assume there is essentially no expression at these spots, or should I
use cel files and re-normalize the data? Use absolute calls? Please
advise. Many thanks in advance.
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