Size of two scRNA-Seq conditions
0
0
Entering edit mode
16 months ago
Chris ▴ 290

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!

scRNA-Seq • 759 views
ADD COMMENT
2
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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?

enter image description here

enter image description here

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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 😅.

ADD REPLY
0
Entering edit mode

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?

ADD REPLY

Login before adding your answer.

Traffic: 2358 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6