hi, I’m trying to take from my cellenics the normalized expression matrix file from one of my treatments “X” and use SingleR to more specifically annotate my clusters for specific cell types. When I look at the csv file, the first column is a series of numbers from 1-- 50000, assuming genes identified. the second column has gene names. The third column and beyond has a sequence in the top row, and then a number in the column somewhere. which seems to be the number of cells for that cluster, interms of the number of columns it has. the file name is “cluster0.csv.gz” (as an example). In R, I was able to load SingleR, and then the reference database “immgen”, but I can’t seem to figure out how to write out the program to take my file and compare it to the reference database “immgen”, and so forth. It gives me an error as soon as I try to use Single R. saying an unused argument. Help Please, do I need to modify the cluster0.csv.gz file before running it in Single R? AND developers? It would be wonderful if you could include a simple module to combine what you have with Single R, instead of just ScType Immune cells (for example). ScType is too basic.
Hi Julie,
It sounds like you’re on the right track with your analysis. The normalized expression matrix you downloaded from Cellenics is a comma-separated file, formatted with genes as rows and individual cells as columns. Each entry in the matrix represents a normalized expression value for a gene in a specific cell. This format should be compatible with SingleR, which requires a numeric matrix with genes as rows and cells as columns.
To ensure everything is set up correctly, please double-check how you’re reading the matrix into R. Which function are you using for this? It’s important to confirm that row and column names are read as expected, as these will be crucial for SingleR’s matching process.
If you’re still encountering errors after verifying the matrix loading process, could you please share more details about the commands you’re using and the specific errors you’re seeing? This will help us understand what might be going wrong.
Thanks for your suggestion about integrating SingleR more closely with Cellenics.
Looking forward to helping you resolve this!