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- Assignment:
- Read variancePartition paper
- Apply it to ImmVar dataset and describe what you learned about biology of gene expression
- How would you apply this framework to a biological question you are interested in?
- # variancePartition
- https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1323-z
- # Data from ImmVar (below) used in Figure 4
- # Original data is described here:
- doi:10.1126/science.1249547
- doi:10.1016/j.smim.2015.03.003
- Here are the data
- # data are here
- https://hoffmg01.u.hpc.mssm.edu/ImmVar/
- user: rnaseq
- password: immvar
- This is just formatted data we downloaded from GEO. Everything was open and public to begin with.
- # read data
- info = readRDS("info.RDS")
- ppData = readRDS("exprObj.RDS")
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