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CIBERSORTx error (error in rep(2, size * length(cells) -1)) : invalid 'times' argument

Hi all, I am brand new to using CIBERSORTx for cell type deconvolution. I am trying to create a signature matrix from a single-cell reference matrix, but I am encountering this error:

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

Here is an example of what my single-cell reference matrix looks like: single-cell reference matrix

Any advice would be greatly appreciated! Thank you in advance.

deconvolution rna-seq cibersortx cibersort
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updated by zhbyrd • zhbyrd • written by Mr. George • Mr. George

What are the dimensions of your single-cell reference matrix?

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written by Aspire Aspire

Hi, George. I hope you are well. I am having the same problem. I want to ask you if you resolved it. Thank you so much for your answer.

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written by Amairani • Amairani

Hi Amairani! I was wondering if you resolved it at all?

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written by zhbyrd • zhbyrd

Hi, George! I am also having the same problem. i was wondering if you have found a solution. Thank you.

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written by zhbyrd • zhbyrd

1 answer

I was just troubleshooting this error. It happens when you (most likely) tried to use averages for each cell type instead of replicates. You need at 2 replicates for each cell type.

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written by Andrew • Andrew

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