text: user4876: I'm getting the following error in a DESeq2 analysis and I can't seem to figure out the issue:
  Error in `assays<-`(`*tmp*`, withDimnames = withDimnames, ..., value = `*vtmp*`) :  please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x, withDimnames=FALSE)) <- value' when the dimnames on the supplied assay(s) are not identical to the dimnames on RangedSummarizedExperiment object 'x'
  Here is my code:
  library(DESeq2)
  library(edgeR)
  
  url <- "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE63310&format=file"
  utils::download.file(url, destfile="GSE63310_RAW.tar", mode="wb") 
  utils::untar("GSE63310_RAW.tar", exdir = ".")
  files <- c("GSM1545535_10_6_5_11.txt", "GSM1545536_9_6_5_11.txt", "GSM1545538_purep53.txt",
             "GSM1545539_JMS8-2.txt", "GSM1545540_JMS8-3.txt", "GSM1545541_JMS8-4.txt",
             "GSM1545542_JMS8-5.txt", "GSM1545544_JMS9-P7c.txt", "GSM1545545_JMS9-P8c.txt")
  for(i in paste(files, ".gz", sep=""))
    R.utils::gunzip(i, overwrite=TRUE)
  
  files <- c("GSM1545535_10_6_5_11.txt", "GSM1545536_9_6_5_11.txt", 
             "GSM1545538_purep53.txt", "GSM1545539_JMS8-2.txt", 
             "GSM1545540_JMS8-3.txt", "GSM1545541_JMS8-4.txt", 
             "GSM1545542_JMS8-5.txt", "GSM1545544_JMS9-P7c.txt", 
             "GSM1545545_JMS9-P8c.txt")
  
  x <- readDGE(files, columns=c(1,3))
  
  samplenames <- substring(colnames(x), 12, nchar(colnames(x)))
  
  colnames(x) <- samplenames
  group <- as.factor(c("LP", "ML", "Basal", "Basal", "ML", "LP", 
                       "Basal", "ML", "LP"))
  x$samples$group <- group
  
  #DESeq2 Analysis
  phenodata <- new("AnnotatedDataFrame", data = data.frame(celltype = x$samples$group))
  counts <- x$counts
  ids <- c(1,3,4,6,7,9)
  
  tmpcounts = counts[, ids]
  tmpph = as(phenodata[ids, ], "data.frame")
  rownames(tmpph) <- colnames(tmpcounts)
  
  dds = DESeqDataSetFromMatrix(countData = tmpcounts, colData = tmpph, design = ~ tmpph$celltype)
  
  Here are my package versions
  > packageVersion("DESeq2")
  [1] ‘1.30.1’
  
  > packageVersion("SummarizedExperiment")
  [1] ‘1.20.0’
  
  
  user-1: What works is:
  dds = DESeqDataSetFromMatrix(countData = data.frame(tmpcounts), colData = tmpph, design = ~celltype)
  
  Mind the data.frame() around the count data object (which was a matrix) and removal of tmpph$ for the design because design should reference one or more columns of the colData. In newer versions of DESeq2 that by the way works without the data.frame() but I am not sure why. You might want to dig that out yourself, looking at the source code of how exactly the package (SummarizedExperiment) feeds data as an assay into a SummarizedExperiments object.
  
original_text: 4876: <p>I'm getting the following error in a DESeq2 analysis and I can't seem to figure out the issue:</p>
  <p><code>Error in `assays&lt;-`(`*tmp*`, withDimnames = withDimnames, ..., value = `*vtmp*`) :  please use 'assay(x, withDimnames=FALSE)) &lt;- value' or 'assays(x, withDimnames=FALSE)) &lt;- value' when the dimnames on the supplied assay(s) are not identical to the dimnames on RangedSummarizedExperiment object 'x'</code></p>
  <p>Here is my code:</p>
  <pre class="lang-r prettyprint-override"><code>library(DESeq2)
  library(edgeR)
  
  url &lt;- &quot;https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE63310&amp;format=file&quot;
  utils::download.file(url, destfile=&quot;GSE63310_RAW.tar&quot;, mode=&quot;wb&quot;) 
  utils::untar(&quot;GSE63310_RAW.tar&quot;, exdir = &quot;.&quot;)
  files &lt;- c(&quot;GSM1545535_10_6_5_11.txt&quot;, &quot;GSM1545536_9_6_5_11.txt&quot;, &quot;GSM1545538_purep53.txt&quot;,
             &quot;GSM1545539_JMS8-2.txt&quot;, &quot;GSM1545540_JMS8-3.txt&quot;, &quot;GSM1545541_JMS8-4.txt&quot;,
             &quot;GSM1545542_JMS8-5.txt&quot;, &quot;GSM1545544_JMS9-P7c.txt&quot;, &quot;GSM1545545_JMS9-P8c.txt&quot;)
  for(i in paste(files, &quot;.gz&quot;, sep=&quot;&quot;))
    R.utils::gunzip(i, overwrite=TRUE)
  
  files &lt;- c(&quot;GSM1545535_10_6_5_11.txt&quot;, &quot;GSM1545536_9_6_5_11.txt&quot;, 
             &quot;GSM1545538_purep53.txt&quot;, &quot;GSM1545539_JMS8-2.txt&quot;, 
             &quot;GSM1545540_JMS8-3.txt&quot;, &quot;GSM1545541_JMS8-4.txt&quot;, 
             &quot;GSM1545542_JMS8-5.txt&quot;, &quot;GSM1545544_JMS9-P7c.txt&quot;, 
             &quot;GSM1545545_JMS9-P8c.txt&quot;)
  
  x &lt;- readDGE(files, columns=c(1,3))
  
  samplenames &lt;- substring(colnames(x), 12, nchar(colnames(x)))
  
  colnames(x) &lt;- samplenames
  group &lt;- as.factor(c(&quot;LP&quot;, &quot;ML&quot;, &quot;Basal&quot;, &quot;Basal&quot;, &quot;ML&quot;, &quot;LP&quot;, 
                       &quot;Basal&quot;, &quot;ML&quot;, &quot;LP&quot;))
  x<span class="math-container">$samples$</span>group &lt;- group
  
  #DESeq2 Analysis
  phenodata &lt;- new(&quot;AnnotatedDataFrame&quot;, data = data.frame(celltype = x<span class="math-container">$samples$</span>group))
  counts &lt;- x$counts
  ids &lt;- c(1,3,4,6,7,9)
  
  tmpcounts = counts[, ids]
  tmpph = as(phenodata[ids, ], &quot;data.frame&quot;)
  rownames(tmpph) &lt;- colnames(tmpcounts)
  
  dds = DESeqDataSetFromMatrix(countData = tmpcounts, colData = tmpph, design = ~ tmpph$celltype)
  </code></pre>
  <p>Here are my package versions</p>
  <pre><code>&gt; packageVersion(&quot;DESeq2&quot;)
  [1] ‘1.30.1’
  
  &gt; packageVersion(&quot;SummarizedExperiment&quot;)
  [1] ‘1.20.0’
  </code></pre>
   -1: <p>What works is:</p>
  <pre class="lang-r prettyprint-override"><code>dds = DESeqDataSetFromMatrix(countData = data.frame(tmpcounts), colData = tmpph, design = ~celltype)
  </code></pre>
  <p>Mind the <code>data.frame()</code> around the count data object (which was a matrix) and removal of <code>tmpph$</code> for the design because design should reference one or more columns of the colData. In newer versions of DESeq2 that by the way works without the <code>data.frame()</code> but I am not sure why. You might want to dig that out yourself, looking at the source code of how exactly the package (SummarizedExperiment) feeds data as an <code>assay</code> into a SummarizedExperiments object.</p>
  