Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argument

Question

[Pumla]

Hello everyone,

I'm currently using CIBERSORTx to create a new matrix for my single-cell RNA-seq dataset. I aim to use CIBERSORTx to generate a reference, but when I attempt to run it, I encounter the following error:

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Errors were encountered in CIBERSORTx configuration, run aborted:

Error in rep(2, size * (length(cells) - 1)) : invalid 'times' argument Calls: CIBERSORTxFractions -> makeRefandClassFiles Execution halted

I'm trying to create the necessary files using R studio and then uploading them on cibersort, but I need help understanding the exact format that CIBERSORTx expects for the reference. I think the issue might be with how I'm preparing my input files, but I'm not sure how to resolve it.

Has anyone encountered this issue or have suggestions on how to correctly format my reference or matrix files to avoid this error?

Any advice or guidance would be greatly appreciated!

Thanks in advance!

Answer 1

[jared.andrews07]

Without posting at least a few lines of your input files, nobody is going to be able to help you. It's also not clear whether you're trying to run through the browser web server or via the Docker image.

The tutorials are quite clear as to how the input files need to be formatted.

[Pumla]

This is the error i have:

and this is my data:

[GenoMax]

Please avoid posting screenshots of text data. You can copy/paste and then format the text as code using 101010 button in the editor window.

[jared.andrews07]

Well, the issue is what it says. You're saying your reference data is single cell, but there's only a single cell for each cell type. It expects more than 1, as (length(cells)) - 1 is zero, which is an obvious problem. You might be able to say it's bulk RNA-seq if you only have one sample.

Again, it seems like you may want to read the tutorials more closely.