pachterlab/bp_2020_2

log(x+1) and log(1+x)

bp_2020_2's Issues

Suggestion: using scvi frequency

Hi Sina,

Great work again! I noticed the BP_2020 paper used SCVI for investigating the similarity (or difference) in ACE2. I am not sure if you also looked at using the expected frequency parameter (rho) defined in SCVI (~ relative expression of a gene within a cell) between 3 and 24 months samples.

The rho-based comparison recapitulates the message of the paper (I am assuming you would have played around with it already). Here's a colab version based on your notebook: https://colab.research.google.com/drive/1t8qaqtb0G6YBH8fedlhfWm5Pz2JeJ0Tf?usp=sharing I used SCVI's DE framework to get a p-value.

Thanks for writing this and for making everything reproducibly available!

Saket

ACE2 not DE - compositional effect

Hi Sina and Lior,

First, I absolutely agree with your main points about problems with log1p (which is why I've developed the sctransform R package) and detection rate as a useful proxy for expression level (assuming negligible sequencing depth differences).

However, I don't think the statement "it is clear that ACE2 has significantly lower mRNA expression in the lungs of aged mice than young mice" is accurate given the data. When clustering the cells, and looking at ACE2 expression (or detection) per cluster across the two age groups, I don't see significant differences. But there is a significant difference in which age group contributes to the ACE2-expressing clusters. For example 74% of the cells for the main ACE2 cluster (AT2 cells I guess) come from age 3 samples, when overall only 55% of the cells come from that age group. Overall there is an enrichment for the age 3 group in the top 7 clusters when ranked by ACE2 detection rate.

So the differences presented in Fig1b could be explained by these compositional differences, and perhaps a more accurate statement would be that 'young mice have significantly more cells of type x, y and z'.

Edit: I just noticed Zhang et al. actually address the same point

We also noticed another preprint manuscript (Booeshaghi and Pachter, 2020) which drew a seemingly different conclusion from our analysis in the expression of gene ACE2. However, certain differences do exist in the analysis from the two groups. First, the major conclusion in our study only focuses on the Ace2 expression within three cell types, which do not consider any other cell types in the data, while the other manuscript evaluated the proportion of Ace2-expressing cells in all cell types and found that younger mice had a higher overall proportion. Second, the reason we chose the presented “within-cell-type” comparison is that the proportion of each cell type is likely to alter between different groups (age groups in this case) and would affect the assessment of gene expression level.

Any comments or clarifications from your side?

Cheers,
Christoph

PS: my analysis notebook