Filtering very low genes counts across all libraries
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@humberto_munoz-10903
Last seen 6.1 years ago

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

gene filtering • 653 views
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@james-w-macdonald-5106
Last seen 9 hours ago
United States

Your last line is

RG <= RG[keep, , keep.lib.sizes=FALSE]

instead of

RG <- RG[keep, , keep.lib.sizes=FALSE]

 

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@humberto_munoz-10903
Last seen 6.1 years ago

Thanks a lot

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@humberto_munoz-10903
Last seen 6.1 years ago

BTY how I can delete the repeated sample names in RG$samples?  

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If you want to add a comment, click on the ADD COMMENT button and add in the box that appears. The Add your answer box below is intended for answers, not comments.

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.

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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

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You need to tell model.matrix where to find the Time and Treat variables

design <- model.matrix(~ Time + Treat, RG$samples)

Please 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.

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