Using CIBERSORTx on Mouse RNAseq Data

Question

[newbie]

Hello,

I am completely new to this type of work, and really need help in understanding how to approach this (I've never used CIBERSORT before). My supervisor has given me an excel file full of RNAseq data from mouse tumors. There are a total of 12 samples (6 controls & 6 tumors) with the gene names on the left column. She wants me to figure out if we can use CIBERSORTx on mouse data. I've followed the CIBERSORTx tutorials with their practice files, and while it appears very straightforward regarding human data, I feel I don't have enough of a thorough understanding of the concepts to translate it to mouse data. I hope that makes sense. I tried imputing cell fractions on the mouse data using the signature matrix files already uploaded by CIBERSORT and it gives an error. I made sure to clean up the mouse data (removed any duplicates or blanks, left only the gene names on the left, the samples to the right, and saved as a .txt file). I tried replacing the mouse gene names with the human equivalents, but still get the same error:

Error in if (max(Y) < 50) { : missing value where TRUE/FALSE needed Calls: CIBERSORTxFractions -> runrmbatchBmode -> CIBERSORTxFractions Execution halted

What does this error mean? Is it possible to use CIBERSORTx on mouse data? Are there any other tutorials or instructions anywhere that I can follow to better understand? Please help!

EDIT: I'm sorry if these are really dumb questions to ask. I'm ignorant to cibersort.

Answer 1

[FrankStarling]

I am new to cybersort as well. You can use mouse bulk RNA-seq data, but blindly using "signature matrix files already uploaded by CIBERSORT" would be weird to do in my opinion. Try to find mouse single cell datasets that are relevant to your bulk RNA-seq data using celldex and scRNAseq packages. Then use this to create a signature matrix. There are many for mouse (maybe even more than human) but pick one that is going to provide useful cell type information for deconvolution of bulk data. I would also read through this([SOLVED] How to build a table with gene expression per cell type with Seurat ?) post thoroughly and also read the attached links in the comments of that post.

Unrelated to OPs question, but a problem I am running into is that I receive this message when running CIBERSORTx online

WARNING: reaching max number of iterations

CIBERSORT deconvolution advice this post reccomneds using docker (which I am waiting for) or to split the signature matrix into smaller parts. If anyone has expierenced this issue with the online versions please let me know.

[newbie]

Thank you! I appreciate your reply so much! I will look into all of this.