I am trying to filter low genes counts across all libraries with the suggested commands from edgeR, but an error in the type of comparison appears. Any help will be appreciated.
> files <- dir(pattern="*\\.csv$")
> group<- c(1,2,2,3,3,4,4,5,5,6,6,7,7)
> RG<- readDGE(files, group=group, labels=NULL)
> RG$samples
files group lib.size norm.factors
CO21Hour CO21Hour.csv 1 11198927 1
CO224Hours CO224Hours.csv 2 11294624 1
Light1Hour Light1Hour.csv 2 12454641 1
Light24Hours Light24Hours.csv 3 8668049 1
NaCl1Hour NaCl1Hour.csv 3 6550245 1
NaCl24Hours NaCl24Hours.csv 4 11475584 1
NaNO31Hour NaNO31Hour.csv 4 10521157 1
NaNO324Hours NaNO324Hours.csv 5 9045265 1
pH1Hour pH1Hour.csv 5 11850679 1
pH24Hours pH24Hours.csv 6 9275761 1
Reference1 Reference1.csv 6 2911654 1
Temperature1Hour Temperature1Hour.csv 7 11726524 1
Temperature24Hours Temperature24Hours.csv 7 8120990 1
> keep <-rowSums(cpm(RG)>1) >=2
> RG<= RG[keep, , keep.lib.sizes=FALSE]
Error in RG <= RG[keep, , keep.lib.sizes = FALSE] :
comparison of these types is not implemented
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As to your question, I don't see any repeated sample names. And you wouldn't want to delete repeated sample names in RG$samples, because they pertain to the samples in your DGEList.
Thank you again. My DGEList has 13 samples, ( 6 conditions with 1HR and 24 HRs and a reference), and I am trying to create the design matrix using and additive linear model, but I got an error with the object Time using the below commands. How I can overcome this error?
> design <-model.matrix(~Time+Treat)
Error in eval(expr, envir, enclos) : object 'Time' not found
> rownames(design)<-colnames(RG)
Error in rownames(design) <- colnames(RG) : object 'design' not found
> design
Error: object 'design' not found
You need to tell
model.matrixwhere to find theTimeandTreatvariablesPlease don't take offense, but it also seems like you would benefit from boning up on some of your basic R chops, too. There are many online tutorials available now to help, too.