Closed mycecilia closed 1 month ago
Hi and thanks for using CytoTRACE 2,
From the messages, it looks like none of your input genes mapped to the model features (("0 input genes mapped to model genes"). Could you please provide some more details about your input to help us understand the issue better?
species
argument to be "human".Please let us know, and if none of these appears to be the root of the issue we will be happy to investigate it further.
Hi and thanks for using CytoTRACE 2,
From the messages, it looks like none of your input genes mapped to the model features (("0 input genes mapped to model genes"). Could you please provide some more details about your input to help us understand the issue better?
- Does your input have the correct format, such as having genes as rows and cells as columns, with row and column names set accordingly?
> data[1:5,1:5]
5 x 5 sparse Matrix of class "dgCMatrix"
CELL1_N2 CELL2_N2 CELL3_N6 CELL4_N4 CELL5_N3
ZH01G00010 . 0.3781146 5.4610153 1.74801 .
ZH01G00240 . 0.6151951 0.0000000 . 0.8525815
ZH01G00750 . . 0.1654955 . .
ZH01G00020 . . 1.1650430 . .
ZH01G00420 . 0.6445649 2.1085691 . .
This is how my expression data look. Row names and column names are gene and cell IDs respectively.
- What species data does your input dataset contain? If your input is a human dataset please make sure to specify the
species
argument to be "human".
The data is from a crop. Not a model species.
Please let us know, and if none of these appears to be the root of the issue we will be happy to investigate it further.
Thank you for your response!
The data format you provided appears to be correct. However, the genes in your input do not overlap with the model features or the orthology mapping supported by our tool, which raises the issue we saw of having no genes mapped. CytoTRACE 2 was specifically developed for use with mouse and human data, and it accepts gene names in MGI and HGNC nomenclatures accordingly. It has not been trained or tested on plant data, so we cannot guarantee results for your case.
Sorry for the inconvenience. Please let us know if we can assist you further!
I got an error message when runing the following lines:
After doing a little digging in the source code, it seemed that the fast mode generated 15 subsamples but it's somehow causing this error. Could you help check this bug? Thank you.
Shiyu