Celltypist showing invalid expression matrix about celltypist

[ChuanXu1]

@aditya-sarkar441, as I downloaded and checked that dataset - please remove the proteome expression in that data, by command such as adata = adata[:, ~adata.var_names.str.startswith("AB_")]

[aditya-sarkar441]

ok. why do we remove this proteome data ?

I got these cell types : ILC, Tcells, Monocytes, B cells. Why am I not getting NK and subtypes of T cells (CD4T, CD8T) ?
Also how can i keep only those cells which are predicted as T cells ?

[ChuanXu1]

@aditya-sarkar441, the prediction is purely based on gene expression, so proteome data should be removed. There should be subtypes showing up, did you select the right model (for example, Immune_All_Low)?

[aditya-sarkar441]

Yeah, I selected Immune_All_High Get Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Chuan Xu ***@***.***> Sent: Monday, March 14, 2022 8:23:50 PM To: Teichlab/celltypist ***@***.***> Cc: Aditya Sarkar ***@***.***>; Mention ***@***.***> Subject: Re: [Teichlab/celltypist] Celltypist showing invalid expression matrix (Issue #14) @aditya-sarkar441<https://github.com/aditya-sarkar441>, the prediction is purely based on gene expression, so proteome data should be removed. There should be subtypes showing up, did you select the right model (for example, Immune_All_Low)? — Reply to this email directly, view it on GitHub<#14 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ANQQQYUNLVW7L66HQARFKWLU75HH5ANCNFSM5QUPGZPA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[aditya-sarkar441]

@ChuanXu1 My Postdoc mentor is telling me that celtypist can predict dozens of cell types. I am not sure how to do this. Can you please help me with this ?

This is the command I'm using :
pred_cont = celltypist.annotate(nature_cont, model = 'Immune_All_High.pkl', majority_voting = True)

[ChuanXu1]

@aditya-sarkar441, as I said, you can choose the "Immune_All_Low.pkl" model instead of "Immune_All_High.pkl"

[aditya-sarkar441]

Ok thanks, I'll try this out.