Cibersort input data

Question

[Maryam]

Hello everynone. Could you please guide me. I have an expression matrix that I have filtered and normalized it by edgeR and limma packages. Can I use this for cibersort? Or I have to use PFKM or TPM for cibersort?

Answer 1

[Penny]

They have specify this in their tutorials. Go to their website and click on menu -- tutorial.

[Maryam]

Thanks for your response.

Answer 2

[DareDevil]

You can use the expression matrix that you've filtered and normalized with edgeR and limma for CIBERSORT, but it is generally recommended to use TPM or FPKM values for CIBERSORT input. This is because CIBERSORT was originally designed to work with TPM/FPKM normalized data, which account for gene length and sequencing depth, making them more comparable across different samples.

If you want to proceed with your edgeR/limma normalized data, ensure that the normalization and filtering process hasn't drastically altered the expression profiles in a way that could affect the relative abundance estimates that CIBERSORT relies on. If you're concerned, you might consider recalculating TPM values from your raw counts.