Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • DESeq2 plotPCA combine replicates

    By default, the plotPCA function in DESeq2 plots the replicates separately. Is there a way to combine replicates so that there is only one dot per group? There does not seem a built-in option for that and it's not obvious to me by looking at the source.

  • #2
    As it performs a PCA, that wouldn't really be possible.

    Comment


    • #3
      hi id0,

      There is a collapseReplicates() function in DESeq2 if you want to combine technical replicates.

      ... and you could create a new DESeqDataSet with this just for plotting.
      Last edited by Michael Love; 06-17-2014, 09:12 AM.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Exploring the Dynamics of the Tumor Microenvironment
        by seqadmin




        The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
        07-08-2024, 03:19 PM
      • seqadmin
        Exploring Human Diversity Through Large-Scale Omics
        by seqadmin


        In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
        06-25-2024, 06:43 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 07:20 AM
      0 responses
      23 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-16-2024, 05:49 AM
      0 responses
      38 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-15-2024, 06:53 AM
      0 responses
      44 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-10-2024, 07:30 AM
      0 responses
      41 views
      0 likes
      Last Post seqadmin  
      Working...
      X