Error in DESeq(dds) : is(object, "DESeqDataSet") is not TRUE
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Entering edit mode
@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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