Hello,
This package really helped my workflow from the ficture output to answering the biological questions of interest, so thank you for making and sharing it!
I also wanted to let you know that for the MHCI (or MHC I) gene, the spatula output using a CosMx RNA dataset and the Ficture decod_xxx_pixel output has an "I" character in the Count column (instead of an integer) and the gene is mislabeled as MHC instead of MHC I (see screenshot below, where the fourth column corresponds to the "Count" field). I assumed most of the counts were ones, but I can't really know from the table. I wonder if this has to do with some character matching issue? And if it should/could be fixed. I also should note that in the ~1k CosMx gene set that I worked with there were issues only with this gene.
Best,
Hello,
This package really helped my workflow from the ficture output to answering the biological questions of interest, so thank you for making and sharing it!
I also wanted to let you know that for the MHCI (or MHC I) gene, the spatula output using a CosMx RNA dataset and the Ficture decod_xxx_pixel output has an "I" character in the Count column (instead of an integer) and the gene is mislabeled as MHC instead of MHC I (see screenshot below, where the fourth column corresponds to the "Count" field). I assumed most of the counts were ones, but I can't really know from the table. I wonder if this has to do with some character matching issue? And if it should/could be fixed. I also should note that in the ~1k CosMx gene set that I worked with there were issues only with this gene.
Best,