I would like to compare RNA seq data obtained from plant A with that of Arabidopsis thaliana. I exposed my plant to 24hrs of cold with 12hrs of light and 12hrs od dark conditions. I want to compare the data set of plant A with the dataset of Arabidopsis thaliana that is exposed to exactly the same conditions. However, In order to do the comparisons I would need to download the data for Arabidopsis thaliana from GEO dataset (pubmed).
I was wondering how valid is it to do this, because although the the two different plants are exposed to the same conditions, they are still two different experiments carried out using two different profiling technologies and at different age?
In my opinion, you can compare your results with similar experimental procedures, depending on what question you want to ask.
If you just want to validate your results by comparing current knowledge and yours, then i think it is fine.
If you want to draw conclusions, then caution
Obviously, the platforms are very important, since you will possibly have much more differentially expressed genes from RNAseq compared to microarray, for example (depending on the system).
Thank you Rohan and Louis for your input. The experiment is carried out on both from the same tissue (leaf). I have serached the GEO data set thoroughly and found no experiment where RNA seq has been carried out on arabidopsis thaliana with similiar conditions. Does it then make it OK to compare with microarray?
Yes you can, but bear in mind what question you want to ask before comparing.
I did this kind of comparison, and albeit they was significant overlap between my RNAseq datasets and microarray ones (between 60-80% common), there is still a significant portion not overlapping. But this question "why it is different" is easily tackled right?= different system,but leading to a majority of common genes
Many thanks Louis, that most helped. I am actually trying to see if the same genes respond similarly between the two plants and so far I am not having much luck. Thanks for responding though.
The last answer to this question was sent in April 17, 2015.
And currently? Are there tools that allow comparing RNA-Seq data generated by different laboratories? For example: suppose I want to compare liver cancer RNA-Seq data generated with Illumina technology in a German lab against transcriptomic data from lung cancer and ovarian cancer, also sequenced using Illumina, and generated by an England lab and a Japanese lab, respectively.
What do you advise me?
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