NA values of count matrix in class DESeqDataSet
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maleknias • 0
@maleknias-14032
Last seen 4.0 years 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 :

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)

>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!!

rna-seq recount • 1.4k views
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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

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Hi,

I just wanted to check in and see if you've resolved this question. If not, please post a reproducible example so I and others can help you.

Best, Leonardo

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Amit ▴ 10
@f8ae0436
Last seen 5 months ago
Netherlands

I got trapped in a similar problem but found a solution by myself. In my case, extra space after count matrix data was the reason for this problem, after deleting those spaces until the last value of count matrix data my problem was solved.

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Best, Leo