CIBERSORTx error: 'x' must be an array of at least two dimensions

Question

[Jie]

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.

[Basti]

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

[Jie]

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?

[Basti]

You can use dput(head(yourdataframe), it will output something like structure(...)and we will be able to reproduce your issue. Additionally if you can paste the CIBERSORT code line you ran it will be ok

[Jie]

Sorry,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..

[Sara]

I have a same problem as you, could you figure out the problem? May you guide me as well!

[kkj3083]

I also have same problem... any updates?

[Sara]

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!