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How do you compare expression in Microarray

Microarray reference gene

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4 replies to this topic

#1 chaghaleh

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Posted 13 June 2013 - 06:24 AM

How do you compare expression in Microarray?
In qPCR, we use reference genes as control and they should have the same or very similar CT values.

How about Microarray?

#2 mdfenko

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Posted 13 June 2013 - 10:25 AM

do a 2-color hybridization. one will be your control and the other your experimental sample
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#3 pcrman

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Posted 14 June 2013 - 01:24 PM

IF you are talking about single array, for every gene on the array, there is an intensity value which is used for expression analysis. So the intensity value can be used as sort of absolute quantification.

#4 mdfenko

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Posted 17 June 2013 - 03:53 AM

if you perform a 1 color hybridization, then you add use a spike-in at a specific ratio to rna in the starting sample (at least, with agilent microarrays).
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#5 Winegarden

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Posted 12 July 2013 - 11:03 AM

Microarrays are ratiometric rather than absolute. They are non-quantitative unlike qPCR. The signal obtained from a probe spot is proportional to the amount of RNA originally present. But due to differences in GC, labelling efficiency and a number of other issues, two genes with the same number of copies in a sample could give a different signal intensity. For that reason - you can only compare a gene to itself.

For example, if you have two samples - A and B and look at the expression of the gene neu, you can say that NEU was more highly expressed in A vs B. However if you are also interested in ESR1 you could not say NEU was more highly expressed that ESR1 just because it had a higher signal.





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