Help with droplevels in Deseq2
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bjen731 • 0
@2586ad17
Last seen 6 days ago
United Kingdom

Hi, I am currently using the DEseq2 package to carry out differential gene expression. When i try to drop levels it gives me an error message saying " no applicable method for 'droplevels' applied to an object of class "character". Can you please explain how I can fix this please? Also I would like some more info on the function 'droplevels' and how to correctly use it in an example please as I am still not sure if I am using it in the correct context.

Thank you!

dds1 <- DESeqDataSetFromMatrix(countData = countdata,
                               colData = colData,
                               design = ~ Celltype+Treatment+Celltype:Treatment)

#subset the  relevant columsn from full dataset, Call it dds1a

dds1a <- dds1[,dds1$Subset == "classical"]

# quick check to see we have the correct samples extracted

as.data.frame(colData(dds1a))

# Droplevels 
dds1a$Celltype <- droplevels( dds1a$Celltype)

#Error in UseMethod("droplevels") : 
  no applicable method for 'droplevels' applied to an object of class "character"
droplevels DESeq2 • 194 views
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ATpoint ▴ 970
@atpoint-13662
Last seen 16 hours ago
Germany

It means that this column of the data.frame is a character and not a factor, and only factors have levels. Actually, if the colData are not factorial you do not have to do anything after the filtering because DESeq2 will convert to factors when running `DESeq()` DESeqDataSet()(or its derivates when starting from matrix or other input formats) automatically. it will print a message when doing so.

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The conversion is at the dataset creation step, e.g. DESeqDataSetFrom....

Any variables in the design which are characters will be converted to factors at that step.

I would check what class() the variables are before and after. You can always just make sure you provide factors to DESeq2, and avoid the character variable problem on your end.

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That makes more sense, thank you very much!

Also, as I am still very new to this field, how would I ensure that the variables are provided as a factor to deseq2 to avoid any issues later on?

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DESeq2 and Bioconductor assume some familiarity with basic R functions, I'd recommend watching a few videos on basics of R, in particular reading about characters and factors. This will be a more efficient way to go forward.

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This here is what you should read, from Hadley Wickham (that's the RStudio/tidyverse/ggplot/magrittr/reshape2 dude) -- short enough to read in a few hours, yet extensive enough to get most essentials:

http://adv-r.had.co.nz/

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