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Danko-Lab / TED

a fully Bayesian approach to deconvolve tumor microenvironment
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Could I use this method to infer cell type from samples which are not tumor samples, likes untreated and treated samples? #24

Open Jihong528 opened 2 years ago

Jihong528 commented 2 years ago

Hello, very great method! But I have normal and treated mouse hypothalamus scRNA-seq data and I wonder could I use this method on my data? Also, could sex bias affect the inference results? I mean, could I use female scRNA-seq data to inference female bulk RNA-seq data, male scRNA-seq for bulk RNA-seq data? Or I can merge female and male scRNA-seq data together and inferecne all the bulk RNA-seq data? Thanks a lot for your help.

Jihong528 commented 2 years ago

Hello, I try my data on the website and I don't know how to solve this error, could you help me check the input data format?

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 240 100 119 100 121 1830 1861 --:--:-- --:--:-- --:--:-- 3692 Loading required package: TED Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': no method for coercing this S4 class to a vector Calls: source ... .local -> as.matrix -> as.vector -> .handleSimpleError -> h Execution halted % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 242 100 119 100 123 1652 1708 --:--:-- --:--:-- --:--:-- 3315

tinyi commented 2 years ago

Hello, very great method! But I have normal and treated mouse hypothalamus scRNA-seq data and I wonder could I use this method on my data? Also, could sex bias affect the inference results? I mean, could I use female scRNA-seq data to inference female bulk RNA-seq data, male scRNA-seq for bulk RNA-seq data? Or I can merge female and male scRNA-seq data together and inferecne all the bulk RNA-seq data? Thanks a lot for your help.

Thank you for your interest in our work. If we assume there is no sex-specific transcription on genes from somatic chromosomes, you can merge the female and male scRNA-seq and then exclude genes from sex chromosomes (please refer to the vignette of the cleanup.genes function for details ). Otherwise, you may deconvolve using scRNA-seq from the matched sex.

tinyi commented 2 years ago

Hello, I try my data on the website and I don't know how to solve this error, could you help me check the input data format?

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 240 100 119 100 121 1830 1861 --:--:-- --:--:-- --:--:-- 3692 Loading required package: TED Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': no method for coercing this S4 class to a vector Calls: source ... .local -> as.matrix -> as.vector -> .handleSimpleError -> h Execution halted % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 242 100 119 100 123 1652 1708 --:--:-- --:--:-- --:--:-- 3315

I will forward your question to our web developer to follow up.