I did RNAseq (single end) for a drug treatment (Drug A) on a cell line to look for the gene expression changes. From the literature, i found some Microarray data on the same cell line treated with other drugs (Drug B, C, D).
I analysed the data of microarray data of this Drug B,C, D samples separately using the limma package and got the differential expressed (DE) gene set Similarly i analyzed RNAseq data using Deseq2 to get the DE geneset. i would like to compare this DE genesets from different treatments to identify the common and unique genes for every treatment.
Here are the questions/doubts that raise in my mind,
1. Can we make the comparison between microarray DE and RNAseq DE ? (having aware that microarrays have defined probe set correspond to only few genes)
2. If we can compare, do they have to be analyzed in a similar way?
3. If they can be analysed similar way, how to make the cross platform comparison to show statistically that these DE which are common in this two or more treatments and these genes are specific for only this treatment?
I have gone through some threads of discussion in the forum but have not answered my questions.
Please feel free to ridicule and suggest me
Thanks in advance