Question: Best way to analyze multiple treatments using DESeq2?
gravatar for michael.frech
19 months ago by
michael.frech0 wrote:




I am analyzing my small RNA seq data which contains 6 samples in total and includes two controls and 3 different treatments. In addition, one treatment has two different time points, so my controls also have two different time points. My coldata looks sth like this:

  condition type
sample 1

treatment 1

2 h 

sample 2

treatment 1 4 h
sample 3


2 h
sample 4


4 h
sample 5

treatment 2

2 h
sample 6 treatment 3

2 h



Now I am wondering how to analyze the data. Should I set a reference level for the first ctrl and run the full dataset and later repeat the analysis using the second ctrl as a reference level, or should I split the dataset to each individual one by one comparison, or should I omit setting a reference level and simply use the contrast argument in the results function? Or is this a case where the multi-factor design function should be applied?

Of course, I know that this kind of analysis is only for exploratory purposes, as I do not have biological replicates included. 

In the end, I would like to come up with a heat map showing the treatment differences compared to their respective controls. As I do not want to show all genes, I will have to order in a way to show the same genes for each condition, but on the other hand, I want to show the relevant genes for each condition. Any suggestions how to order/ cluster?

One last question: On a windows machine I didn't have problems with plotting the resLFC in an MA plot using "plotMA", whereas my mac seemed to have problems. The Error message was: "Error from the generic function 'plotMA' defined in package 'BiocGenerics': no S4 method definition for argument 'resLFC' of class 'numeric' was found"

Thank you in advance!

mirna deseq2 rna-seq • 348 views
ADD COMMENTlink modified 19 months ago by Michael Love25k • written 19 months ago by michael.frech0
Answer: Best way to analyze multiple treatments using DESeq2?
gravatar for Michael Love
19 months ago by
Michael Love25k
United States
Michael Love25k wrote:

We don’t have any support for no replicate analyses.  What in particular are you interested in comparing here? You can just run the counts through vst() and compute LFC between individual samples using simple subtraction.

ADD COMMENTlink written 19 months ago by Michael Love25k
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