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Is it possible to compare two samples that their RNA was extracted by two different methods?

In analysis of RNAseq data, is it possible to compare samples that their RNA was extracted by two different methods? for example RNA of control was extracted by qiagen kit and RNA of treatment by TRIZOL method, both samples have high qulity and integrity.

rna-seq
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updated by Ram Ram • written by eyonesi • eyonesi

1 answer

If you have samples of both groups (controls and treated) extracted with both methods, you would be able to use a design in e.g. edgeR with a batch effect. However, if you have only control samples with 1 method and the treated samples with the other method, it is impossible to determine the effect of the batch (=method) or the real biological effect of the treatment.

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written by Benn Benn

This could be an answer - not necessarily a comment ;)

Indeed, you are creating a huge batch effect. During your analysis, you will not know if the difference in gene expression is due to biological effect or due to the different processing of the samples.

And you also cannot compare one sample with another. Make sure you have replicates!

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written by WouterDeCoster WouterDeCoster

Thanks for your guidance.

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written by eyonesi • eyonesi

Thanks for your guidance.

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written by eyonesi • eyonesi

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