Error at the InferLandmark() step about landscent HOT 6 CLOSED

Hi,

Yes, of course. Just remember to make sure the gene identifier is the same with the PPI network. Say if you are using the PPI network in our package, you need to get the homolog gene with human and transfer to EntrezID.

Best,
Weiyan

from landscent.

Hi,

It seems the output Number of significant components = 1 which indicated the error.

This means there probably be some problems with the input matrix, you may need to check the data matrix to see if there anything strange.

Best,
Weiyan

from landscent.

Hi @ChenWeiyan,

Thanks for getting back to me. I couldn’t find missing values or anything else odd in the matrix. Is there anything specific I should be looking for ? Could the small number of cells be an issue ? This is a published dataset and has around 3k cells for 1 sample and 1.5k for the other.

from landscent.

Hi,

The number of cells is fine.

The estimation of Number of significant components is based on a random matrix theory, which works with your input matrix. Since the Number of significant components = 1, it means your data matrix has already been transformed or similar operation.

So you may need to check the matrix stored in InferPotency.o $expMC. Make sure it has the correct information of the integrated data, eg. the correct dimension or expr information.

And also important to check if the SR values are all correctly calculated.

Hope this be helpful.

Best,
Weiyan

from landscent.

Hi,

I was using a transformed matrix which was probably the reason for the error. Before I move forward, I wanted to clarify if a mouse dataset can be used ?

Thanks.

from landscent.

@ChenWeiyan I'll close this issue for now since I won't be working on this project right away. I'll reopen if I still have issues. Thanks for your help.

from landscent.