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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
@James W. MacDonald how should i get that ? any suggestion
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.
@James W. MacDonald I think, the answer is very easy , I should just get the data normalised , Not a rocket science !
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.
@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 .
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.