Ask about ERROR:celltype

[Michael A]

Hello,

Recently I am trying to run cell type analysis (jobID: 605938) using SNP2GENE result (jobID: 603546). I check my data has MAGMA result and I have unchecked ensembl gene ID, it still does work. Even, when I checked ensembl gene ID assumption, it's not working. 

Would you please help me handle this situation?

Michael 

[Tanya Phung]

Hi Michael,

In the FUMA Cell type job, MAGMA was not able to run for the dataset "TabulaMuris_FACS_Tongue". I attached the log here. Note that I do not support MAGMA so if you have a question on why this fails with your dataset, you would need to contact the developer for MAGMA. 

#log

Parsing model specifications...
Inverting gene-gene correlation matrix...
Performing regression analysis...
        testing direction: one-sided, positive (sets), one-sided, positive (covar)
        conditioning on internal variables:
                gene size, log(gene size)
                gene density, log(gene density)
                sample size, log(sample size)
                inverse mac, log(inverse mac)
        conditioning on input variables (no output):
                Average (covar)
        analysing individual variables

        analysing single-variable models (number of models: 2)
        WARNING: analysis failed for 'basal_cell_of_epidermis' (covar); could not invert variable design matrix: variable is collinear with conditioned covariates
        WARNING: analysis failed for 'keratinocyte' (covar); could not invert variable design matrix: variable is collinear with conditioned covariates

ERROR - running gene-level regression: analysis failed for all variables/models

Terminating program.

#endlog

Otherwise, I suggest that you remove this dataset from the analysis and resubmit.

Best,
Tanya