how to determine fold change of gene expression - (Jul/13/2011 )

Hi,

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?

Thanks!
taranaki

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!

May be this R tutorials could be helpful for you

For the basics of microarray analysis and fold change.

http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/

An this one for the heatmaps

http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/heatmap.

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.