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how to determine fold change of gene expression

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#1 Taranaki



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Posted 13 July 2011 - 05:58 AM


I've done a microarray to have a look at the effects of a siRNA-mediated knockdown of my gene of interest. I have checked the expression of some of the deregulated genes with qPCR.

I've seen that some people compare the expression level determined by Microarray and qPCR. However, I do not understand how they calculate the fold change of gene expression for those genes which are covered by several probes on the array. For example, one genes is covered by 5 different probes and therefore you also have 5 different logFC values.

So, how do you calculate the fold change of gene expression from microarray data?


Edited by Taranaki, 13 July 2011 - 05:59 AM.

#2 toejam


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Posted 21 July 2011 - 03:48 AM

hi taranaki,

i'm far from being an expert in microarrays, especially since i just started analysing them very recently. do you observe any differences in the logFC of the same gene that is covered by 5 different probes? in principle you shouldn't. if i'm not mistaken, you are looking at 5 different bits of the same gene by using 5 different probes, which means that the logFC of the same gene should be the same over all of them.

when you detect interesting changes in gene expression by the microarray, then you confirm that data more precisely via qpcr. i hope this helps. good luck!
"When there's no more room in hell the dead will walk the Earth"

#3 Felipillo



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Posted 18 April 2012 - 02:24 PM

May be this R tutorials could be helpful for you

For the basics of microarray analysis and fold change.


An this one for the heatmaps


Also, there is a recient method published here

RankProd: Hong et. al.
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis,
Bioinformatics, 22 (22), 2825-2827.
Chance favors the prepared mind
Louis Pasteur.

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