Closed Zepeng-Mu closed 1 year ago
Although I realized that this might an issue with SeuratObject
.
I actually figured out the problem is with the formatting of column names in the matrix. Switching the colnames seems to avoid the error message. This is strange because I did not run in to the same error in previous analysis with the same data.
It seems that GT-1337
does not work although both GT1337
and 09359-20
works fine.
Turned out in my case the column names of a matrix is an array rather than character. https://github.com/GreenleafLab/ArchR/issues/1999#issuecomment-1761987935
I recently ran into a similar problem, with the same error message for a supplied 5 x 5
matrix, but this actually happened while following the ArchR tutorial. I don't fully understand your solution above @Zepeng-Mu and had opened an issue here. How would the code in ArchR Tutorial Section 8.1 have to be amended to avoid this bug?
Hello, I ran into this error in my analysis while trying to create a seurat object.
After some digging around, I really cannot find the problem but I have two weird examples. Example 1:
when I supplied this
5x5
matrixseuratATAC <- Seurat::CreateSeuratObject(counts = mat)
I got the error message.Example 2:
This is also a small 5x5 matrix, but running
seuratATAC <- Seurat::CreateSeuratObject(counts = mat)
gives no error.I'm wondering what could be the reason behind different outcomes for these toy examples. There could be something bigger under the hood but I have no clue. This is the session info:
Thanks in advance!