Error in DESeq(dds) : is(object, "DESeqDataSet") is not TRUE
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@1d1b2e76
Last seen 4 weeks ago
United States

Hi Everyone, I am very new to using R,

I want to use the DESeq2 package to look at breast cancer data. However, anytime I used the DESeq2 on the dataset that I generated, it gives the following error Error in DESeq(dds) : is(object, "DESeqDataSet") is not TRUE I do not know what to do. Any help will be much appreciated

This is everything that I did below

Code should be placed in three backticks as shown below

rawCounts <- read.delim("/Users/ng/Desktop/BC_RNA_Dseq/E-GEOD-52194-raw-counts.tsv")sampleData <- read.delim("/Users/ng/Desktop/BC_RNA_Dseq/E-GEOD-52194-experiment-design.tsv")

head(sampleData)
head(sampleData)
keep <- c("Run", "Sample.Characteristic.clinical.information.","Sample.Characteristic.individual.","Sample.Characteristic.disease.")
sampleData_3 <- sampleData[-c(2),keep]
rownames(sampleData_3) <- sampleData_3$Run colnames(sampleData_3) <- c("Run", "BC_Subset", "ID", "Disease") sampleData_3$ID <- factor(sampleData_3$ID) rawCounts$Gene.Name <- NULL
head(rawCounts)
str(rawCounts)
rownames(rawCounts) <- rawCounts[,1]
rawCounts_3 <- rawCounts[,-1]
rawCounts_3 <- rawCounts_3[, rownames(sampleData_3)]
all(colnames(rawCounts_3) == sampleData_3\$Run)

dds <- DESeqDataSetFromMatrix(countData = rawCounts_3,
colData = sampleData_3,
design = ~ ID, tidy = FALSE,
ignoreRank = FALSE)
dds <- dim(dds[rowSums(counts(dds)) > 5, ])

# include your problematic code here with any corresponding output

dds <- DESeq(dds)

# please also include the results of running the following in an R session

Error in DESeq(dds) : is(object, "DESeqDataSet") is not TRUE

sessionInfo( )

DESeq2 • 120 views
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Entering edit mode
@mikelove
Last seen 4 hours ago
United States

I think it's where you say:

dds <- dim(...)


Because dim returns integers not a dataset.

If you are stuck like this, a helpful function is class(). This is because class(dds)` would have given you a clue what's happening.

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Entering edit mode

Thank you so much, Michael. Your was very helpful

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