Geo2r rna seq analysis

Question

[angiannak]

Hello guys,

I am relative new to RNA-seq data analysis. I would appreciate if anyone could ask my question.. To my understanding after you run RNA-seq analysis pipeline the information u get is whether the group under investigation (let's call it disease group) differentially expresses a gene in contrast to control. Is it possible to know which samples of my disease group overexpress the gene of interest?

Is it acceptable to use tpm normalized expression values from GEO2r and somehow understand which samples from my disease group over-express the gene of interest?

[ATpoint]

Please google for using normalized counts for differential analysis. This has been asked a great many times before. Generally it is preferred to use raw counts. Websites like biojupies can give you that from public studies or packages like recount at Bioconductor, in case you don't want to download and process the raw fastq files.