<p>DESeqDataSetFrom<strong>Matrix</strong> but a SummarizedExperiment is not a matrix. Use the function <code>DESeqDataSet()</code> instead and make sure the <code>design</code> argument is followed by a <code>=</code>.</p>

CC BY-SA 4.0
2023-01-26T21:20:00.910Z
2023-01-26T21:20:00.910Z
ATpoint
<p>I'm tryig to perform RKM normalization on raw counts for RNA-Seq Data:</p>
<pre><code>counts_data &lt;- exprs181517[,-1]
#Setting title col to rownames for pheno data 
rownames(pheno.data181517) &lt;- NULL
rownames(counts_data) &lt;- exprs181517[,1]
phenoColData &lt;- tibble::column_to_rownames(pheno.data181517, &quot;title&quot;)
colnames(counts_data) &lt;- rownames(phenoColData)
#Defining the design column
designCol &lt;- as.data.frame(phenoColData$characteristics_ch1)
rownames(designCol) &lt;- rownames(phenoColData)

#Creating a summarized experiment
se &lt;- SummarizedExperiment(list(counts=counts_data), colData=phenoColData)

DESeqDataSetFromMatrix(se, design ~ designCol)
</code></pre>
<p>but I keep getting this error:</p>
<pre><code>Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix':
    no method for coercing this S4 class to a vector
</code></pre>

<rna-seq><bioconductor><normalization>
Error while using SummarizedExperiment() in R
# Error while using SummarizedExperiment() in R

(Asked by: username_0 on 2023-01-26)

I'm tryig to perform RKM normalization on raw counts for RNA-Seq Data:
counts_data <- exprs181517[,-1]
#Setting title col to rownames for pheno data 
rownames(pheno.data181517) <- NULL
rownames(counts_data) <- exprs181517[,1]
phenoColData <- tibble::column_to_rownames(pheno.data181517, "title")
colnames(counts_data) <- rownames(phenoColData)
#Defining the design column
designCol <- as.data.frame(phenoColData$characteristics_ch1)
rownames(designCol) <- rownames(phenoColData)

#Creating a summarized experiment
se <- SummarizedExperiment(list(counts=counts_data), colData=phenoColData)

DESeqDataSetFromMatrix(se, design ~ designCol)

but I keep getting this error:
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix':
    no method for coercing this S4 class to a vector

**Tags:** rna-seq, bioconductor, normalization

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## 1 answers

### Answer by username_1 on 2023-01-26. Score: 2

DESeqDataSetFrom**Matrix** but a SummarizedExperiment is not a matrix. Use the function `DESeqDataSet()` instead and make sure the `design` argument is followed by a `=`.


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