PCA of Kallisto output 17-05

Raw data (kallisto-Sleuth output)

Sleuth output was converted to matrix format, transposed (to fit Prcomp format) and filtered (sum of gene expression across all samples had to be above 5 tpm)

so <-readRDS("//jic-hpc-data/Research-Groups/Cristobal-Uauy/Anna/sleuth_clipNclean_rds")
matrx <- sleuth_to_matrix(so, "obs_norm", "tpm")
mx <- t(matrx)
length(colnames(mx))

## [1] 298774

mx2 = mx[,colSums(mx) > 5]
length(colnames(mx2))

## [1] 103862

Filtering of outlier samples

I removed F4, H2 and G2, because they were extreme outliers in PCA graphs

length(rownames(mx2))

## [1] 27

length(rownames(G2))

## [1] 24

PCA

G2.pca <- prcomp(G2, center = TRUE, scale. = TRUE)

PCA of Kallisto output 17-05

AB

19/05/2020

Raw data (kallisto-Sleuth output)

Filtering of outlier samples

PCA

Color by Tissue

Color by Waddington stage

rTSNE graphs (color by tissue)