Question: Filtering low intensity probes of microarray data
gravatar for prathyushareddy87
3.2 years ago by
prathyushareddy870 wrote:

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.

R • 2.0k views
ADD COMMENTlink modified 3.2 years ago by h.mon31k • written 3.2 years ago by prathyushareddy870

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.

ADD REPLYlink written 3.2 years ago by cpad011214k
gravatar for h.mon
3.2 years ago by
h.mon31k wrote:

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.
ADD COMMENTlink written 3.2 years ago by h.mon31k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1553 users visited in the last hour