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Hi! I am new in single cell analysis and I have a sce object where I ask for:
librarySizeFactors(sce)
And I get this:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1 1 1 1 1 1
I don't have a clue what's happening really :( Also, is there a book to read about sc analysis? I am having trouble with all the concepts
Thank you
Thank you for you answer :)
I have been reading the OSCA book, but my question is more about what i got from the library size factor function. I know that what I did is the total sum of counts per cell, so what I got means that I have one count per cell on each cell?
Normally, one would expect a mean size factor of 1, as all scran-based methods will scale the size factors are scaled so that they have a mean of 1. This ensures that the magnitude of the normalized values are, on average, comparable to that of the counts.
In this case, I suspect that the matrix was already normalized by library size (e.g., CPMs or equivalent), such that the column sums for all cells are equal. As such, all size factors end up being equal to 1 after the average is forced to 1.
Thank you for your answer it helps me a lot! :)