Search
Question: NA values of count matrix in class DESeqDataSet
0
gravatar for maleknias
6 weeks ago by
maleknias0
maleknias0 wrote:

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!!

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by maleknias0

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

ADD REPLYlink written 6 weeks ago by Leonardo Collado Torres540
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 344 users visited in the last hour