Rui:RNAseq analysis on HL101

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RNAseq analysis on HL101[edit]

  • Kun's lab note on 9.7.11 [1]
  • Dinh's note on PCA analysis
> A = read.table("/home/kunzhang/SingleCell/Data/HL101/Mm_Indx3-15_FPKM_matrix_no_NA.txt", header=TRUE, row.name=1)
> pca1 = prcomp(t(A), scale=TRUE)
> hist(pca1$rotation[,1])
> sd(pca1$rotation[,1])
[1] 0.01028287
> cutoff = qnorm(p=0.05, mean=0, sd=0.01028287)
> cutoff
[1] -0.01691382
> higher = rownames(A)[which(pca1$rotation[,1] > 0.017)]
> lower = rownames(A)[which(pca1$rotation[,1] < -0.017)]
> write.table(file="Mm_Indx3-15_genes_lowWeightsPC1.txt", lower)
> write.table(file="Mm_Indx3-15_genes_highWeightsPC1.txt", higher)