I would take this opportunity to encourage using different tools. Cibersortx is not open, its source code has never been published. That has implications for reproducibility. Say the website shuts down tomorrow forever, you can never reproduce results. It is beyond me why authors do not put their code on GitHub, reviewers and editors should penalize that by immediate rejection of tool papers.
CIBERSORTx error: 'x' must be an array of at least two dimensions
Hi everyone,
I'm new here.
I'm using CIBERSORTx to build my own signature matrix for brain related cell type. But every time I run it, it always encountered the following error:
Error in base::rowMeans(x, na.rm = na.rm, dims = dims, ...) :
'x' must be an array of at least two dimensions
Calls: CIBERSORTxFractions ... buildSignatureMatrix -> rowMeans -> rowMeans ->
Execution halted
I'm soooo confused cause my file format is right and complete. And I can't find the original source R code for CIBERSORTx..... Does anyone encounter this before? What's the issue would be? I can send my files to see what's the problem if needed. Thank you sooo much in advance.
1 answer
For those still looking for the answer about this, I just figured out that you need to have replicates for it to work.
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As the problem is likely to be data specific, indeed I suggest you to share an example of your dataset so that we could test what is going wrong. Thanks
Hi Basti,
Below is the snipping of my files. One is the expression matrix of different cell types in brain, which I got from GSE73721. The other one is their phenotype info.
So Sorry I'm not familiar with biostars. Is this kind sharing OK? If not, how can I share files with you on this platform? Or via e-mail?
You can use
dput(head(yourdataframe), it will output something likestructure(...)and we will be able to reproduce your issue. Additionally if you can paste the CIBERSORT code line you ran it will be okSorry,Basti... I can't understand you... I use their website of CIBERSORTx, I can't find the CIBERSORT code line you mean. The file contains 15000+ rows and 24 columns, I still don't know how can I share you these files. So sad... T^T If you can see my email address from my profile, could we communicate through e-mail? I would further try how to show my data in Biostars..
I have a same problem as you, could you figure out the problem? May you guide me as well!
I also have same problem... any updates?
And another question how did you create your Ref matrix for the brain, which you shared here? You mentioned that you downloaded from GSE73721, but I noticed that the table of GSE73721 is different from the table you shared here. Did you remove some columns, or is it another table that I do not know? I appreciate your help as I also need to use this table. Thank you in advance!
Unfortunately, I do not have an answer. Instead, I want to report exact same error message when I attempted to run CibersortX. I would like to know who has got an answer. My single cell RNAseq file does not have replicate, I am not sure whether this causes the error. Thanks in advance.
I´m having the same problem here described. Any updates on how to solve this?