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shyhihihi / MERCI

MERCI for tracing of mitochondrion transfer between single cancer and T cells
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error when running MERCI_LOO_MT_est #4

Open zhuangxuehan opened 6 months ago

zhuangxuehan commented 6 months ago

Hi,

When I running: RNA_rank <- MERCI_LOO_MT_est(cell_exp, reciever_cells=Donor_cells, donor_cells=Receiver_cells,organism='Human')

I got the error message: Error in svm.default(x, y, scale = scale, ..., na.action = na.action) : NA/NaN/Inf in foreign function call (arg 4)

I checked the cell_exp, it is ok, cause if I swap the Donor_cells and Receiver_cells, i.e., RNA_rank <- MERCI_LOO_MT_est(cell_exp, reciever_cells=Donor_cells, donor_cells=Receiver_cells,organism='Human')

it works.

Would you give me any suggestions?

shyhihihi commented 6 months ago

Hi Zhuangxue，

If the expression of all mitochondrial genes for some receiver cells in cell_exp is consistent with zero value, SVM will return an error message as you paste. Please check the expression of mitochondrial genes for every receiver cell. If you find any cells that have no expression in any of the mitochondrial genes, please remove them from the dataset. Regarding this question, we recently updated the MERCI package, and the new version of the MERCI_LOO_MT_est function should automatically remove those unqualified input cells. You can try the new version of the MERCI package and run it again. Let me know if you still have any problem. Thanks!

zhuangxuehan commented 6 months ago

Hi Zhuangxue，

If the expression of all mitochondrial genes for some receiver cells in cell_exp is consistent with zero value, SVM will return an error message as you paste. Please check the expression of mitochondrial genes for every receiver cell. If you find any cells that have no expression in any of the mitochondrial genes, please remove them from the dataset. Regarding this question, we recently updated the MERCI package, and the new version of the MERCI_LOO_MT_est function should automatically remove those unqualified input cells. You can try the new version of the MERCI package and run it again. Let me know if you still have any problem. Thanks!

Thank you so much! I removed the cells without mitochondrial gene expression and it works!