Rui:RNAseq analysis on HL101
Jump to navigation
Jump to search
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)