PCA Plot in Single-cell RNA-seq Data

Question

[Darya]

Hi everyone,

I need some help with a PCA plot I generated from my single-cell RNA-seq data. My supervisor thinks it looks strange, suggesting issues with normalization or data distribution. I've checked normalization and data distribution, but everything seems fine. Yet, the PCA plot still looks off.

Could you take a look at the plot and share your thoughts? Have you seen anything like this before? Any ideas on what might be causing it or how to fix it? Thanks a lot for your help!

[ATpoint]

It shows that cell cycle is the driver of variation. Why is this strange? A lot of genes are differential between these phases.

[Darya]

Thank you for your reply. I agree with you about the cell cycling phases, my concern lies more with the overall shape of the PCA plot. It appears to deviate from what is typically observed in similar analyses, prompting suspicions about potential issues with normalization or data preprocessing.

[ATpoint]

I don't know what "shape" generally to expect. I see nothing that worries me here.

[Darya]

I agree with you. It's good to hear there's nothing to worry about. Thanks again for your reply!