Log-Fold Change in RNA-seq

Question

[thepurplebluesociety]

Hello everybody, I am quite new to RNA-seq. I am using DESeq2 for differential expression analysis and I am at a stage where I have to identify for each cell type the 10 highest expressed, specific genes (>5-fold higher). I have 3 conditions (3 cell types) and each condition has ( 3, 5, 2 samples). Can you give me advice on how to do it?

Answer 1

[padwalmk]

Hi, First check the tutorial from the DESEq it has explained everything very nicely.

You can follow the following steps for now.

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1. First you have to extract all three contrast result using the result <- data.frame(results(dds, contrast = "blah_blah"))
2. Then subset according to your criteria subset(result, criteria > "whatever")