Filtering low intensity probes of microarray data

Question

[prathyushareddy87]

Hi All,

I have a question related to the analysis of the microarray data. In the process of differential gene expression analysis, filtering low probe intensities is very crucial. The array chip I am analyzing presently is HuGene1.0 ST array. I am using oligo package in R to analyze and rma normalization method. Can anyone recommend how to filter low probe intensities and how to derive a cut-off to know that these are the probes with low intensities?

Thanks a lot.

[cpad0112]

post normalization, you would get normalized intensity values. You can choose a cutoff to filter out probes with lower intensities. Before you filter out probes, look at the probe intensity distribution across the chips.

Answer 1

[h.mon]

You can use apt-probeset-summarize from the Affimetrix Power Tools to calculate a "detected above background" probability:

   dabg         Calculates the p-value that the intensities in a
                probeset could have been observed by chance in a
                background distribution. Used as a substitute for
                standard absent/present calls when mismatch probes 
                are not available.