Open AbhijeetRPatil opened 1 year ago
Hi Abhijeet R Patil,
Thank you for your question.
To investigate co-expression of Gene A with other genes, we include normalized expression of Gene A in the design matrix. You could include only those genes of which you want to investigate the co-expression in the count matrix. To illustrate, I give an example script below for the co-expression analysis of APOE in the paper using a Seurat Object.
covs = @.** # pbmc is a Seurat Object of the single-cell data set covs$apoe_e = counts[match('APOE',rownames(counts)),]/as.numeric(as.character(covs$nCount_RNA))1e3
many zeros, you might use other normalized methods such as Pearson residuals which can be obtained from NEBULA apoe_m = aggregate(apoe_e~orig.ident,covs,mean) # get subject-level mean of the expression of APOE covs$apoe_e_c = covs$apoe_e - apoe_m[match(covs$orig.ident,apoe_m[,1]),2] # subtract subject-level mean from normalized expression (This step is optional, depending on whether you want cell-level co-exp only.) pred = model.matrix(~nFeature_RNA+rprot+percent.mt+apoe_e_c,covs) # create a design matrix, adjusting for covariates like number of non-zero features, ribosomal and mitochondria mrna percentage id = as.numeric(factor(as.character(covs$ind),levels=unique(as.character(covs$ind)))) re = nebula(counts,id,pred=pred,offset=covs$nCount_RNA) # the logFC and p-value of apoe_e_c give information about the co-expression between APOE and all genes in the count matrix @.**@.'
Best regards,
Liang
On 5/10/2023 5:56 PM, ABHIJEET R PATIL wrote:
Hi, Thanks for developing this awesome package for measuring differential expression analysis in scRNA-seq through mixed modelling! In the manuscript, I saw the co-expression analysis. Can you please let me know where I can find the relevant code in the package. Thanks for your help!
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Hi, Thanks for developing this awesome package for measuring differential expression analysis in scRNA-seq through mixed modelling! In the manuscript, I saw the co-expression analysis. Can you please let me know where I can find the relevant code in the package. Thanks for your help!