Question: Cross platform gene expression comparison and threshold choice
1
gravatar for elb
14 months ago by
elb170
Torino
elb170 wrote:

Hi guys, I have a question about how to choose a reasonable threshold to define genes to be expressed (not differentially expressed but simply expressed) to compare gene expression measurements from different platforms. In other words I have to check if my list of genes is expressed using an RNA seq dataset, using a data set of one-color microarrays and another of two colours microarrays. If for RNA Seq is generally "accepted" (but I know that it depends on the experimental condition) an rpkm >1 I don't know how to set a threshold for microarrays. Any suggestion about this?

Thank you in advance

ADD COMMENTlink modified 14 months ago by Devon Ryan93k • written 14 months ago by elb170
3
gravatar for Devon Ryan
14 months ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

There is no generally accepted threshold in RNA-seq. You can come up with a threshold using zFPKMs, but even that is a bit hand-wavy. For microarrays, you generally check either that the PM signal is sufficiently above the MM signal and/or that a probe is sufficiently above that of the background control probes. Not that these are sort of apples and oranges measurements, in that they're really not comparable.

ADD COMMENTlink written 14 months ago by Devon Ryan93k
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