I have to plan a bioinformatic study on a plant. Microarray data is available for various stress treatments (drought, cold, osmotic and flood stress) on root and shoot tissues. I am a bit confused as to which tissue is more important for the perception of stress and its direct effect. I want to start with one of them as of now, since the study will get too complicated with so many stress conditions and tissues. I am not from a botany field and look for some thoughts. Sorry if my question sounds silly.Thanks a lot.
I know this is not what you want to hear back, but I think you should go with all the samples/replicates at once. Only this way you will have the highest possible statistical power to claim the results that (hopefully) you'll have in the end.
When it comes to microarrays and RNASeq, also, it is important to remember that these are mostly whole-transcriptome techniques, therefore the way they are thought to be used is more like "sequence all > analyze all > fish for specifics" than the opposite.
I would use all of them, feed them to a proper pipeline (there are many, not my duty to suggest you one) and see what has a good score/p-value. If you had something in mind before doing the microarrays you probably would have assessed only a subset of the genes, and not the whole transcriptome. So go for both tissues and see what pops out!