text: user2005: I am trying to use DESeqDataSetFromTximport function from DESeq2 package to construct dds object:
  dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Group)
  
  And somehow it is giving me the following error:
  
  Error in rownames<-(*tmp*, value = c("ENSMUSG00000000001", "ENSMUSG00000000003",  : 
      invalid rownames length
  
  I used the same code for other datasets but for the current one it is somehow not working. My sampleTable looks like this:
         ID      Group
  1    de_1 denervated
  2    de_2 denervated
  3    de_3 denervated
  4    de_4 denervated
  5   den_5       sham
  6    ho_1        IgG
  7    ho_2        IgG
  8    ho_3        IgG
  9    sh_1       sham
  10   sh_2       sham
  11   sh_3       sham
  12   sh_4       sham
  13   sh_5       sham
  14 VLA_10  anti-VLA4
  15 VLA_12  anti-VLA4
  16  VLA_7  anti-VLA4
  
  txi was formed in the following way:
  k = keys(txdb, keytype = "GENEID")
  df = AnnotationDbi::select(txdb, keys = k, keytype = "GENEID", columns = "TXNAME")
  tx2gene = df[, 2:1]  # tx ID, then gene ID
  txi <- tximport(names, type = "salmon", tx2gene = tx2gene)
  
  Any suggestions would be greatly appreciated
  
  user4410: The same error occurred to me with DESeq2_1.22.2 using R 3.5.0.
  By trial and error, I managed to solve the issue when I updated SummarizedExperiment from 1.10.1 to 1.12.0.
  
  user174: I got exactly the same problem not long ago (see my other question what I tried to do). We used the same function!
  My code ran fine on my HPC but the same code/data failed on my laptop. I later found out I had to upgrade my R to the latest version (3.5.1) and upgrade all my bioconductor packages to the latest. My HPC was on a recent bioconductor docker, so there was no problem.
  Please make sure everything in your environment latest (R, R packages, Bioconductor).
  
original_text: 2005: <p>I am trying to use <code>DESeqDataSetFromTximport</code> function from <code>DESeq2</code> package to construct <code>dds</code> object:</p>
  
  <pre><code>dds &lt;- DESeqDataSetFromTximport(txi, sampleTable, ~Group)
  </code></pre>
  
  <p>And somehow it is giving me the following error:</p>
  
  <blockquote>
    <p>Error in <code>rownames&lt;-</code>(<code>*tmp*</code>, value = c("ENSMUSG00000000001", "ENSMUSG00000000003",  : 
      invalid rownames length</p>
  </blockquote>
  
  <p>I used the same code for other datasets but for the current one it is somehow not working. My <code>sampleTable</code> looks like this:</p>
  
  <pre><code>       ID      Group
  1    de_1 denervated
  2    de_2 denervated
  3    de_3 denervated
  4    de_4 denervated
  5   den_5       sham
  6    ho_1        IgG
  7    ho_2        IgG
  8    ho_3        IgG
  9    sh_1       sham
  10   sh_2       sham
  11   sh_3       sham
  12   sh_4       sham
  13   sh_5       sham
  14 VLA_10  anti-VLA4
  15 VLA_12  anti-VLA4
  16  VLA_7  anti-VLA4
  </code></pre>
  
  <p><code>txi</code> was formed in the following way:</p>
  
  <pre><code>k = keys(txdb, keytype = "GENEID")
  df = AnnotationDbi::select(txdb, keys = k, keytype = "GENEID", columns = "TXNAME")
  tx2gene = df[, 2:1]  # tx ID, then gene ID
  txi &lt;- tximport(names, type = "salmon", tx2gene = tx2gene)
  </code></pre>
  
  <p>Any suggestions would be greatly appreciated</p>
   4410: <p>The same error occurred to me with <code>DESeq2_1.22.2</code> using <code>R 3.5.0</code>.
  By trial and error, I managed to solve the issue when I updated <code>SummarizedExperiment</code> from <code>1.10.1</code> to <code>1.12.0</code>.</p>
   174: <p>I got exactly the same problem not long ago (see my <a href="https://bioinformatics.stackexchange.com/questions/5531/how-should-i-address-batch-effects-in-my-experiment">other</a> question what I tried to do). We used the same function!</p>
  
  <p>My code ran fine on my HPC but the same code/data failed on my laptop. I later found out I had to upgrade my R to the latest version (3.5.1) and upgrade all my bioconductor packages to the latest. My HPC was on a recent bioconductor docker, so there was no problem.</p>
  
  <p>Please make sure everything in your environment latest (R, R packages, Bioconductor).</p>
  