RNA sequencing of two samples
How I can compare the expression value for two genes in the two samples? & What the measure I can use in the comparison have been arrived at?
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B- for bioinformatics •
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If you only have 2 samples, there is a minimal amount of things that you can do. You should still normalise them together and then just look at, for example, ratio of expression for your gene of interest. p-values for a 1 vs 1 comparison make little sense - you would be laughed out of the room if you presented p-values for n=2
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Kevin Blighe
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What kind of data? How many samples? And so on. There are many very good packages with lots of documentation around - like DESeq2 and edgeR - and I feel reading them carefully will answer your questions.