NA values of count matrix in class DESeqDataSet
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maleknias • 0
@maleknias-14080
Last seen 3 months ago

Dear all

Hi

I downloaded a data set in class "RangedSummarizedExperiment" from "https://jhubiostatistics.shinyapps.io/recount/". I want to find differential expression genes. My code is :

>load("~/Downloads/rse_gene.Rdata")

>class(rse_gene)

**[1] "RangedSummarizedExperiment"

attr(,"package")

[1] "SummarizedExperiment"**

>data=colData(rse_gene)

>names= names(colData(rse_gene))

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

>data1=fread("~/Downloads/colData.txt")

>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:

assay(rse_gene)=assay(rse_gene)[complete.cases(assay(rse_gene)),]

 

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

rnaseq recount • 1.6k views
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