Entering edit mode
6 weeks ago
Chris ▴ 70
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.
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.
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?
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.
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 😅.
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?