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Question: single cell RNA seq Differential Expression using MAST
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gravatar for quintanamaster
9 months ago by
quintanamaster • 0
United Kingdom
quintanamaster • 0 wrote:

Hi all,

I'm using MAST package to detect differentially expressed genes in single cell RNAseq datasets. I've used DESeq2 in the past and I know that it selects the reference group for calculating fold changes alphabetically if not pre-defined. I'm struggling to understand if MAST does the same thing? Does it select the reference group for FC calculation alphabetically? It's not very clear from the documentation available.

Thanks in advance for helping,

Juan
sequencing rna-seq next-gen • 668 views
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modified 9 months ago by ATpoint ♦ 44k • written 9 months ago by quintanamaster • 0
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gravatar for ATpoint
9 months ago by
ATpoint ♦ 44k
ATpoint ♦ 44k wrote:

I guess so. The keyword you are looking for is reference level, see https://www.bioconductor.org/packages/release/bioc/vignettes/MAST/inst/doc/MAITAnalysis.html#4_differential_expression_using_a_hurdle_model

The relevel function is what you need as described in the first few lines of code of paragraph 4.
ADD COMMENT • link modified 9 months ago • written 9 months ago by ATpoint ♦ 44k

Thanks ATpoint!

I'm running the code from the Seurat vignette as below:

head<- FindMarkers(Combined, ident.1 = "Ast_2", ident.2 = NULL, test.use = "MAST") View(head) write.csv(head, "../Desktop/Hyp_DE_Ast22.csv", row.names = TRUE)

It doesn't let me use the "relevel" option so that's why I was wondering if it does the selection alphabetically by default?

ADD REPLY • link written 9 months ago by quintanamaster • 0

It looks like you are actually using Seurat, not MAST. Although you are using the MAST test, you are using Seurat's interface, not the native MAST one. Thus, you have to refer to Seurat documentation.

If you are not sure what the order is, check the average expression (AverageExpression()) and then you can see which group is higher or lower.

ADD REPLY • link written 9 months ago by igor ♦ 12k
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