getting error with DEseq2
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Nemo ▴ 80
@nemo-7332
Last seen 3.6 years ago
India

Hello, 

I am getting an error like this 

Error in DESeqDataSet(se, design = design, ignoreRank) : 
  some values in assay are not integers

Based on previous questions, I tried to solve it but I could not. So let me tell you how to imported the data etc 

countdata<-read.table("data.txt",header=TRUE,row.names=1)

conds<-as.factor(c("Treated","Control"))

coldata <- data.frame(row.names=colnames(countdata), conds)

dds=DESeqDataSetFromMatrix(countData=countdata,colData=coldata,design=~conds)

The following are more information about countdata 

 

deseq2 • 12k views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

The error says some of your values are not integers, and your data.frame looks like this:

> head(countdata)
         Control    Treated
gene1 0.00842815 0.01090013
gene2 0.25059516 0.98230798
gene3 0.29728284 0.15692372
gene4 0.30918591 0.36842593
gene5 0.31040477 0.47786814
gene6 0.31833954 0.40623309

Which makes sense, because none of those values are integers! If you want to use DESeq2 to analyze your data, you need to get count data which will be strictly integer values.

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@James W. MacDonald how should i get that ? any suggestion 

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I don't know. Where did you get these data to begin with? I would imagine you should be talking to whomever you got the data from.

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@James W. MacDonald I think, the answer is very easy , I should just get the data normalised , Not a rocket science ! 

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No. The data you input has to be integers. Whatever you think normalization is going to do, rest assured it won't. Do you know what an integer is? Maybe that's the problem. If you don't understand that term, then we will never get anywhere.

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@James W. MacDonald  of course i do. as I said , if I do make them integer as they are now , i'll lose a lot of info. the best is to normalise them and then use the function "as.integer" in R . 

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James is correct.

Do not provide normalized data to DESeq2. 

You need to generate counts using one of the methods described in the documentation:

vignette("DESeq2")

On the very first page of the vignette, after the table of contents, you will find a section called "Why un-normalized counts?" Read this.

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