Downstream analysis for microarray data
Hi, i have done microarray DEG analysis using limma on affymetrix clariom s human data. My samples are cancer vs cancer samples (for learning purpose since i am still a degree student and quite new to bioinformatics). Right now, I have 230 significant probes and already mapped them to gene symbols and descriptions. I'm planning to move on to downstream analysis (pathway analysis) but i'm a bit lost on what should i do next
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Qistina •
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I'd consider finding a toy RNA-seq dataset instead given arrays have largely fallen out of favor. There are dozens of tutorials out there on pathway/enrichment analyses, so you'll need to make your question more pointed if you want help beyond just pointing you at those (clusterprofiler, GSEA, fgsea, sva, camera, enrichr, g:profiler, among others).