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Question: NA values of count matrix in class DESeqDataSet
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gravatar for maleknias
8 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

I use two solution for this problem but both of them were useless:

1- Keep only rows with non-zero counts:

>rse_gene <- rse_gene[rowSums(assay(rse_gene)) != 0, ]

2- Replace the NA value by -9 :

>countdata <- assay(rse_gene)

>replace(countdata,countdata==0,-9)

>coldata <- colData(rse_gene)

>ddsMat <- DESeqDataSetFromMatrix(countData = countdata, colData = coldata, design = ~ disease.status)

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

ADD COMMENTlink written 8 weeks ago by maleknias0

Hi,

Please post code for reproducing the error and the R session information you have. Thanks.

Also, why are you writing the colData() information to a text file and then reading it back into R? Are you editing the colData() information outside R?

Best, Leonardo

ADD REPLYlink written 7 weeks ago by Leonardo Collado Torres560
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