Question: Can I extract absolute gene expression from Illumina beadchip human microarray?
gravatar for tigeradab
4 weeks ago by
tigeradab50 wrote:

I wish to find out actively expressing genes from the llumina HumanHT-12 v4 Expression BeadChip. I also generated the background corrected and normalized signal intensities for every gene in each sample using the normexp function in limma. Is it possible to draw any conclusions related to absolute gene expression from the normalized signal intensities? Is it appropriate to take average of the signal intensities across samples and based on an arbitrary cut-off term some genes to be actively expressing in all samples?

I'm a novice in microarray data analysis. Please help.

ADD COMMENTlink written 4 weeks ago by tigeradab50

No, it is not possibly to draw conclusions about absolute gene expression from array intensities (either raw or normalized).

You can, however, estimate which genes non-expressed, in particular if the array has negative probes, which the Illumina HT v4 Expression BeadChip has. limma has a detectionPValues() to do this.

Check a more detailed discussion at Estimate Absolute Expression Value From Microarray Data

ADD REPLYlink written 4 weeks ago by h.mon30k

Thank you very much for the reply. After filtering non-expressed genes, I also wish to identify coexpressing genes. In this case, can I make use of the normalized signal intensities?

ADD REPLYlink written 4 weeks ago by tigeradab50
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