I am new to bioinformatics and PCA. What I am trying to do is to remove bad cells from a dataset that was obtained with
46 000 of genes (rows) vs
68 000 of cells that are of different types of
C. Elegans that was generated in the following paper.
fontsize <- theme(axis.text=element_text(size=12),
plotPCA(sce, pca_data_input="pdata") + fontsize
I see the following chart:
I suppose that the cells that are going to the left bottom corner are the bad ones since they do not fall into some restricted region. Are there any
R program that can automatically remove the bad cells leaving me with just the majority of cells clustered within an ellipse? I know there is
identify method that allows for clicking and labelling manually cells that I think may be outliers (see this) but I do not like it. I would prefer some program that would do that for me, giving some statistical output of the reliability of the removal of the cells.