Entering edit mode
6.9 years ago
maggiepan
•
0
Hi All,
I wonder if I could combine data generated by different Hiseq platforms, say 2500 vs 4000?
Thanks!
Hi All,
I wonder if I could combine data generated by different Hiseq platforms, say 2500 vs 4000?
Thanks!
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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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.
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?