Question: NA values of count matrix in class DESeqDataSet
gravatar for maleknias
12 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 12 months ago • written 12 months ago by maleknias0

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

ADD REPLYlink written 12 months ago by Leonardo Collado Torres610
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