Hello everyone My doubt is that can we compare the analysis result of different platforms of microarray. I have done d analysis using the GEO.2R the result file contains the pvalue log2FC and gene name. These columns are extracted from the file. Similarly it is done for another study done of different platform. Can we compare the gene names obtained from two different study done on two different platform?
See a similar discussion: What are the requirements to use data generated in other microarray experiments as a control?
Yes, you can compare them. However, I would urge against doing fixed-effects metaanalysis since you shouldn't expect the fold-changes to be the same even if it was the same samples put on two different platforms (in my experience log-fold-changes tend to be extremely similar - even when paralogues are compared across species - for a well designed experiment).
What you could do is define two genesets using the upregd genes and the downregd genes from one dataset and look at the distribution of fold-changes, or p-value ranks for these genesets in the other dataset by GSEA