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Danko-Lab / BayesPrism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
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Mouse or human (?) for option "species" #89

Open yingzhang121 opened 2 months ago

yingzhang121 commented 2 months ago

Hi, I encountered a weird issue while running BayesPrism.

I am working on Mouse data, and the gene names are in the following format:

> head(colnames(sc.dat))
[1] "ENSMUSG00000109644" "ENSMUSG00000007777" "ENSMUSG00000086714" "ENSMUSG00000043644" "ENSMUSG00000020831"
[6] "ENSMUSG00000046683"

After plotting the outlier genes, I started to filter out genes using the cleanup.genes() function.

Below is my error:

> sc.dat.filtered <- cleanup.genes(input=sc.dat, input.type="GEP", species="hs",
+                                   gene.group=c("Rb","Mrp","other_Rb","chrM","MALAT1","chrX","chrY"))
[1] "As the input is a collpased GEP, exp.cells is set to min(exp.cells,1)"
EMSEMBLE IDs detected.
number of genes filtered in each category: 
      Rb      Mrp other_Rb     chrM   MALAT1     chrX     chrY 
       0        0        0        0        0        0        0 
A total of  0  genes from Rb Mrp other_Rb chrM MALAT1 chrX chrY  have been excluded 
A total of  596  gene expressed in fewer than  1  cells have been excluded 

> sc.dat.filtered <- cleanup.genes(input=sc.dat, input.type="GEP", species="mm",
+                                   gene.group=c("Rb","Mrp","other_Rb","chrM","MALAT1","chrX","chrY"))
[1] "As the input is a collpased GEP, exp.cells is set to min(exp.cells,1)"
EMSEMBLE IDs detected.
Error in `[.data.frame`(category.matrix, , gene.group, drop = F) : 
  undefined columns selected

So I checked the help page for cleanup.genes, it says:

species | A character variable to denote if genes are human ("mm") or mouse ("hs"). Currently only these two species are supported.

Does this mean in some of the functions, we should use "hs" for mouse data, and in some functions, we should use "mm" for mouse data?

So confusing.

Best, Ying

tinyi commented 2 months ago

Hi Ying,

Thank you for your interest in our methods. Please note that "MALAT1" is a human gene (an outlier gene in many human cancers). When using species="mm", try not including this gene category.

Best,

Tinyi

On Mon, Jun 17, 2024 at 1:05 PM Ying Zhang @.***> wrote:

Hi, I encountered a weird issue while running BayesPrism.

I am working on Mouse data, and the gene names are in the following format:

head(colnames(sc.dat)) [1] "ENSMUSG00000109644" "ENSMUSG00000007777" "ENSMUSG00000086714" "ENSMUSG00000043644" "ENSMUSG00000020831" [6] "ENSMUSG00000046683"

After plotting the outlier genes, I started to filter out genes using the cleanup.genes() function.

Below is my error:

sc.dat.filtered <- cleanup.genes(input=sc.dat, input.type="GEP", species="hs",

  • gene.group=c("Rb","Mrp","other_Rb","chrM","MALAT1","chrX","chrY")) [1] "As the input is a collpased GEP, exp.cells is set to min(exp.cells,1)" EMSEMBLE IDs detected. number of genes filtered in each category: Rb Mrp other_Rb chrM MALAT1 chrX chrY 0 0 0 0 0 0 0 A total of 0 genes from Rb Mrp other_Rb chrM MALAT1 chrX chrY have been excluded A total of 596 gene expressed in fewer than 1 cells have been excluded

sc.dat.filtered <- cleanup.genes(input=sc.dat, input.type="GEP", species="mm",

  • gene.group=c("Rb","Mrp","other_Rb","chrM","MALAT1","chrX","chrY")) [1] "As the input is a collpased GEP, exp.cells is set to min(exp.cells,1)" EMSEMBLE IDs detected. Error in [.data.frame(category.matrix, , gene.group, drop = F) : undefined columns selected

So I checked the help page for cleanup.genes, it says:

species | A character variable to denote if genes are human ("mm") or mouse ("hs"). Currently only these two species are supported.

Does this mean in some of the functions, we should use "hs" for mouse data, and in some functions, we should use "mm" for mouse data?

So confusing.

Best, Ying

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