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( )
Thank you so much, Michael. Your was very helpful