In vjcitn/CSHstats: discussions and exercises on classical statistics for CSHL 2022

Fast forward

This document shows how SRP045638 can be retrieved and analyzed. We start with filtered and normalized data in the vGene object.

library(edgeR)
library(CSHstats)
data(vGene)
names(vGene)
head(vGene$E[,1:5])

The model matrix is also important:

data(mod)
head(mod)

Here are the top results from the limma-voom analysis:

data(de_results)
options(digits=3)
de_results[1:5, c("gene_name", "logFC", "t", "P.Value", "adj.P.Val")]

This is a little different from the de_results computed in the class document -- because we sort by p and take the most significant results.

Assessing the association "by hand"

The vGene$E structure holds the estimated expression values, and vGene$weights are quantities that measure relative variability of the quantities in E. We can pick a gene of interest and examine the marginal distribution and estimate association.

The top DE gene was "ENSG00000121210.15". Let's make a data.frame with the E values, the covariates, and the weights.

target = "ENSG00000121210.15"
ind = which(rownames(vGene$E)==target)
mydf = data.frame(cbind(KIAA0922=vGene$E[ind,],
      mod[,-1], wts=vGene$weights[ind,]))

Now examine the marginal distribution:

hist(mydf$KIAA0922)

Interesting. There's a big gap in the KIAA0922 expression distribution.

Exercise: Is that true for the "raw" data, or is it an artifact of all the computations we've done?

library(beeswarm)
beeswarm(mydf$KIAA0922, pwcol=as.numeric(factor(mydf$prenatalprenatal)))
legend(.6,6,legend=c("postnatal", "prenatal"), col=c(1,2), pch=19)

Finally, we fit the linear model:

m1 = lm(KIAA0922~.-wts, data=mydf, weights=wts)
summary(m1)
plot(m1, which=2, col=(as.numeric(mydf$prenatalprenatal)+1), pch=19)

vjcitn/CSHstats documentation built on Jan. 9, 2025, 8:37 p.m.