RT-PCR vs Next Gen Sequencing

[NicoBxl]

Hi,

I'm looking after a way to compare ( differential expression ) Next Gen sequencing ( illumina ) and RT-PCR ( Applied TaqMan cards ) in the mirna field. We've the same samples for the two experiments of course.

Anyone has an idea ?

Thanks,

Nicolas

[NicoBxl]

nobody knows ?

[mrawlins]

For comparing samples of Illumina data I would use a Fisher Exact Test on quantile-normalized read counts to get a probability that two samples are the same. I'm not sure how I would do the same comparison for RT-PCR because I haven't done much experimentation with that.

Comparing the Illumina directly to the RT-PCR will be difficult, because they will have different biases, distributions, etc. It would be best to compare two conditions on Illumina and the same two conditions with RT-PCR and see if they get the same or similar differences. You might be able to use some kind of T-test for that, but there may be easier tests to use. It will probably depend quite a bit on your experimental design how to best design the statistical testing.

[krobison]

There are a number of papers in the literature making this comparison; perhaps you should start there?

Try PubMed search for "rna-seq AND (rt-pcr OR qpcr)"

[upendra_35]

Its good to compare the NGS data with QPCR rather than RT-PCR.