Question: NA values of count matrix in class DESeqDataSet
gravatar for maleknias
9 months ago by
maleknias0 wrote:

Dear all


I downloaded a data set in class "RangedSummarizedExperiment" from "". I want to find differential expression genes. My code is :



**[1] "RangedSummarizedExperiment"


[1] "SummarizedExperiment"**


>names= names(colData(rse_gene))

>write.table(data,file="colData.csv", col.names=names,sep="\t",row.names=FALSE)


>colData(rse_gene) =DataFrame(data1)

>colData(rse_gene)$disease.status = as.factor(colData(rse_gene)$disease.status)

>dds <- DESeqDataSet(rse_gene, design = ~ disease.status)

**converting counts to integer mode Error in validObject(.Object) :

invalid class “DESeqDataSet” object: NA values are not allowed in the count matrix In addition: Warning message: In mde(x) : NAs introduced by coercion to integer range**


p.s: I used some functions to  filter rows with NA data, like:



I will be appreciate if any one can help me!!

ADD COMMENTlink modified 9 months ago • written 9 months ago by maleknias0

Looks like the same as this question NA values of count matrix in class DESeqDataSet

ADD REPLYlink written 9 months ago by Leonardo Collado Torres600
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