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Combining high throughput data from Illumina

Hi All,

I wonder if I could combine data generated by different Hiseq platforms, say 2500 vs 4000?

Thanks!

rna-seq hiseq
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updated by Devon Ryan Devon Ryan • written by maggiepan • maggiepan

What does "combine" mean in your analysis? Please be as specific as possible.

For example: If you are doing differential expression analysis with treatment A on HiSeq2500 and controls on HiSeq4000 you are potentially introducing a batch effect.

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written by WouterDeCoster WouterDeCoster

precisely, by 'to combine' I meant to do DE analysis for both set of samples. and yes you are right! it is actually a batch effect question, i would have thought of that, thank you! do I have to do correlation analysis first to check at least whether I can combine the two set of samples for analysis?

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written by maggiepan • maggiepan

1 answer

Sure, though keep in mind that if the library prep was done at different times/by different people/etc. that you have a batch effect to account for.

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written by Devon Ryan Devon Ryan

That is very helpful, thank you!!

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written by maggiepan • maggiepan

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