BALuca

Hi, I suspect that none of the bulk samples are assigned to ecotypes or cell states for a given cell types for this version of sc-ecotyper. Therefore, EcoTyper was crashing...

Dear Verena, Thanks for the clarification. I agree that 134 samples should be enough. Another possibility is that the CIBERSORTx crashes when trying to perform in-silico purification (step 2), therefore...

Hi Verena, 15,000 genes should definitely be enough, and judging by the output you pasted above, step 2 ran "successfully". However, it is puzzling that all cell types fail to...

Hey, can you please send the rank plot you are getting and the configuration file you used, so that we can have a look? You can either post it here...

Hi, We investigated the issue and it seems that different versions of R can give slightly different results for the example data. This is because some EcoTyper steps, including NMF...

Hi, We noticed this behavior when the ecotypes discovered from single-cells are not robust enough. This can happen when the number of scRNA-seq samples used for discovery is small. Two...

Hi, Unfortunately, we do not have access to the CIBERSORTx website. You would need to contact the CIBERSORTx admins for this request. Best, The EcoTyper team

Hi, Apologize for the confusion, there is no requirement to transform microarray data to FPKM/TPM. EcoTyper should work on microarray data as it is. Best, The EcoTyper team

Hi, Apologize for the delay in responding to this. I suspect this error has to do with a formatting issue of the input data. Would you be able to send...

Hi, Would it be possible to send the data you tried, the command line and the R version you used to [email protected], so that we can investigate the issue? Best,...