Paul

Paul's Notes

Understanding the Galaxy Data:

We care about: Fold Change, P-value

Think about total gene expression values and gene functions. Be aware that large gene expression values can be paired with low fold change, but that cn still be significant.

In the data input, the first data set (numerator) and second data set (denominator) order is important to sign of fold change.

Possible tests: M WT vs P WT, disomic vs trisomic

truncation for excel ensembl gene numbers: =left(A1,18)

Potentially helpful DEseq paper: http://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-10-r106

https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf

DEseq2: uses negative binomial distribution to model gene expression "We assume that the number of reads in sample j that are assigned to gene i can be modeled by a negative binomial (NB) distribution, Kij~NB(μij,σ2ij)"