I was wondering if any of you could give me some advice with the following issues:
- All results are different when performing "absolute" deconvolution using legacy CIBERSORT source code R version (no.sumto1 & sig.score), legacy CIBERSORT online tool and the online CIBERSORTx tool (see example copied below). Has there been a change in the code between versions?
- I have very large matrices to deconvolute (up to 780MB). Is it possible to split up matrices for deconvolution of samples I want to compare?
- How does CIBERSORT accomplish to exclude non-hematopoietic genes during signature matrix genetartion? Is there an internal database of "hematopoietic" and "non-hematopoietic" genes? In this case, I am wondering which gene annotation tool and which snapshot thereof was used to define "non-hematopoietic" genes? The reason why I am asking is, that I am concerned this will affect signature matrix generation depending on which annotation tool and version I use for gene annotation of the reference file due to tool-specific annotation differences in gene names (alterantive gene names, novel transcripts etc...) that don't match the CIBERSORT internal record.
- For the imputation of cell fractions, how important is it to match gene annotation of signature and mixture in regard to gene-annotation differences caused by different annotation tools/versions. Do I have to assume that the results are always penalised in case the mixture and signature/reference files were annotated in different labs (with a different annotation tool / version)? How would an annotation difference of more than 15% of genes between signature and mixture affect deconvolution performance?
- Error during the imputation of cell fractions using CIBERSORTx: "WARNING: reaching max number of iterations". What is the cause and how can I solve it?