Question: Log-Fold Change in RNA-seq
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gravatar for thepurplebluesociety
13 months ago by
thepurplebluesociety0 wrote:

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?

rna-seq R • 328 views
ADD COMMENTlink modified 13 months ago by padwalmk100 • written 13 months ago by thepurplebluesociety0
1
gravatar for padwalmk
13 months ago by
padwalmk100
padwalmk100 wrote:

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

You can follow the following steps for now.


  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")
ADD COMMENTlink written 13 months ago by padwalmk100
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