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cailab-tamu / scTenifoldKnk

R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.
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subscript out of bounds #5

Closed Leonrunning closed 3 years ago

Leonrunning commented 3 years ago

Hi Daniel,

It is me again. I have tested knocking out several genes from my datasets and most of them work well except for this one as attached. The function seems to be completed successfully, but one error occurs for the output. Is there any way that we can increase the size of the output matrix for this issue?

Sorry to bother you again on this.

thanks

Leon

"|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06h 10m 43s |================================================================================================================================| 100% Error in [<-(*tmp*, gKO, , value = 0) : subscript out of bounds"

dosorio commented 3 years ago

Hi Leon,

The problem is that you are trying to knock out a gene that is not present in your gene regulatory network. Please double-check the gene is expressed in your cell type or tissue of interest.

Best wishes,

Daniel

Leonrunning commented 3 years ago

Hi Leon,

The problem is that you are trying to knock out a gene that is not present in your gene regulatory network. Please double-check the gene is expressed in your cell type or tissue of interest.

Best wishes,

Daniel

Oh, that make sense. It is expressed at very low level and may be filtered out. Appreciate for your help!

Thanks!

Leon