SVA will just determine the batch covariates that [may] exist in your data, pl. help.

Question

[david_lyon3]

Can someone show me exactly with code since I am a beginner, how does the R package sva determine which covariates exists in a dataset of proteins or genes? Say I have covariates that I need to check eg Age, Sex, Ethnicity, with the main comparisons Disease versus Control and then the data set eg: 1000 genes.

Can someone show me exactly with code needed to test for each of the covariates c("Age", "Sex", "Ethnicity") to see which one is useful to add as a covariate to my Limma contrast?

Title of post taken from reference: Using SVA to correct for covariates in RNA-seq data

Thank you very much in advance

Dave

[rpolicastro]

Their documentation is pretty detailed and includes some vignettes that let you follow along. If you have any specific questions while going through their examples you can post your questions here.

[david_lyon3]

Sorry I dont see an example where it shows for example "covariates c("Age", "Sex", "Ethnicity") to see which one is useful to add as a covariate to my Limma contrast?" Still beginner I am afraid.

Can someone show me exactly with code needed to test for each of the covariates c("Age", "Sex", "Ethnicity") to see which one is useful to add as a covariate to my Limma contrast?

Thank you in advance

[david_lyon3]

Any chance someone can help with this question please?

Thank you in advance