In UPSCb/RnaSeqTutorial: RNA-Seq Tutorial

    startQuest("Differential Expression Analysis - Practical")

    h1("Preformed leaves Differential Expression")

For the practical, you will replicate what we have been doing in the tutorial. However, there are a few twists.

• The data has been quantified with salmon [@Patro2017] instead of kallisto [@Bray2016]. The data is in the folder share/leaf/salmon. When reading the abundance data in, you need to give additional arguments to readAbundance, namely the pattern: *\.sf and the type: salmon.

• The sample information is in share/leaf/doc.

• When creating the ddsobject, you will need to change the design. Take a look at the sample information to devise it. You can provide a design as an argument to the createDESeqDataSet function, using the design argument; e.g. dds <- createDESeqDataSet(counts,samples,design= ...) where you replace ... with the design of your choice.

• Once you will have run DESeq, ask us for which comparison you should look into. Note that we are performing a time series, but all conditions will have been compared to D0. To compare D2 vs. D1, you will need to compare:

"D2 vs. D0" vs. "D1 vs. D0", in other words, since we are on a log scale:

(D2 - D0) - (D1 - D0) = D2 - D1

This is written as an argument to the results function as follows:

res <- results(dds,contrast = list("DevStage_D2_vs_D0","DevStage_D1_vs_D0"))

    endQuest()

UPSCb/RnaSeqTutorial documentation built on Nov. 24, 2020, 12:40 a.m.