Size of two scRNA-Seq conditions

Question

[Chris]

Hi all,

I have scRNA-Seq data from 2 conditions, and 3 samples for each condition. However, the size of each condition is significantly different after reading into R using ReadMtx (360Mb vs 130Mb). Is there anything wrong with that? Seurat objects created from these matrix objects are also significantly different in size.

Thank you!

[rpolicastro]

More important would be the cell QC stats (such as reads per cell and number of unique features detected per cell), the number of cells per dataset, the cellular composition/proportions of each dataset, and and the number of cells per cluster. If these are sufficient and comparable you are probably fine. If for example the smaller dataset is missing a cell type that's important for the analysis that would be an example of sample size effecting the analysis you can do.

[Chris]

Thank you so much for your answer! Here is the structure of 2 matrix objects of two conditions. Condition 1 has 19760 cells meanwhile condition 2 only has 6705 cells. Is that OK?

[rpolicastro]

You need to show the other sample stats I mentioned otherwise I can't provide an answer. Most of those stats are calculated if you follow the default Seurat vignette.

[Chris]

Dataset 1 has 19760 cells and dataset 2 has 6705 cells. I am trying to get the code to get the info you want. I am still trying to learn 😅.

[Chris]

I have QC stat with violin plots n_Feature_RNA, nCount_RNA and percent.mt, not exact numbers. Is that the info we need in this case?