Hello all, I'd like to say thanks to all of you for your work, your data and your code. I'm trying to re-produce the same analysis with given data from GEO. I ran cell ranger with the same version as yours and I found the summaries from mine and yours are identical. However, when trying to merge all subjects into 1 matrix (using readMM and then convert to Seurat object), the total number of cells I had is 27786 while yours is 33547.
I manually summed all number of estimated cells from cell ranger summary (from your provided output at https://github.com/abcwcm/Notaras_MolPsy/tree/main/10x_webSummaries ) and noticed that it should be 27786. May I ask how is it possible to have 33547 cells in your analysis?
# your output
dim(sce)
#[1] 33538 33547
Noted that the number of genes in my output is still 33538.
Thanks again.
Hello all, I'd like to say thanks to all of you for your work, your data and your code. I'm trying to re-produce the same analysis with given data from GEO. I ran cell ranger with the same version as yours and I found the summaries from mine and yours are identical. However, when trying to merge all subjects into 1 matrix (using
readMMand then convert to Seurat object), the total number of cells I had is 27786 while yours is 33547.I manually summed all number of estimated cells from cell ranger summary (from your provided output at https://github.com/abcwcm/Notaras_MolPsy/tree/main/10x_webSummaries ) and noticed that it should be 27786. May I ask how is it possible to have 33547 cells in your analysis?
Noted that the number of genes in my output is still 33538.
Thanks again.