Question: Generate The Affymetrix Array Expression Value Using Incomplete Probe Set
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gravatar for Jian-You
5.7 years ago by
Jian-You0
Jian-You0 wrote:

Hi all,

I'm trying to reannotate the probe of Affymetrix HG U133 plus 2.0 Array. I found some genes I interested in were mapped with less than 11 probes (for example 7 probes). I wanted to generate the expression value of these genes using the imcomplete probe set, but I don't know how to do it. One solution I can think of is to delete the unmapped probe information of the probe set targeting to the gene I interested in from CDF file, and then used the edited CDF file to generate the expression value using affymetrix Expression Console. I successed to generate the expression value using this strategy, but I found that the expression value seems to be positive correlated with the probe number in the probe set, that is, the more probe number I used, the higher expression value I will get. So, I'm not sure whether this solution can generate the right expression value or not. I would appreciate that if anyone can give me advice to handle this problem.

Best, Jian-You Liao

affymetrix • 1.9k views
ADD COMMENTlink modified 5.7 years ago by Sean Davis25k • written 5.7 years ago by Jian-You0

I don't quite understand your problem. Could you try giving an actual example?

If a gene maps to 7 probes instead of 11, why is it incomplete?

ADD REPLYlink written 5.7 years ago by David Westergaard1.4k

I’m sorry for the unclear description. Most probe set of Affymetrix HG U133 plus 2.0 Array has 11 probes, and it use the signal of whole probe set (11 probes) to evaluate the expression level of each gene. I want to use the signal of part of probe (e.g. 7 probes) in a probe set to evaluate the gene expression level, because some genes I interested in can only be mapped with part of probes in a probe set.

ADD REPLYlink written 5.7 years ago by Jian-You0
0
gravatar for Sean Davis
5.7 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

See these pages, for example:

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdfreadme.htm

Just FYI, the expression values between probesets are not comparable, so there really isn't a problem with having different signal with different probe counts. That said, why you are seeing such an effect is probably related to the summarization you are using and I do not know what that step includes.

And this gist might be useful:

<script src="&lt;a href=" rmflight="" 3108891"="">rmflight/3108891"></script>

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by Sean Davis25k
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