Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • sBeier
    replied
    In a way you do not want the replicates to be totally consistent, because then you won't have the possibility to say that a differential expression between conditions is significant, compared to the expression differences in between replicates of the same condition.

    If you used cufflinks to do the differential expression analysis, you can do some nice correlation analysis with cummeRbund.

    Leave a comment:


  • simonandrews
    replied
    I don't think there is going to be a universal answer to this since the degree of correlation between replicates will very much depend on your biological system. Our normal approach is to cluster all of the replicates for all conditions and then see what pattern emerges. What you hope to see is that the replicates for a condition cluster together more closely than samples from different conditions.

    By doing this sort of larger scale clustering you can also then spot samples which are outliers from the whole set and which might have technical problems. You can also potentially spot sample swaps if you have pairs of samples which appear misplaced.

    If there is no real grouping then this doesn't mean the replicates are bad, it just means that the noise in your system is higher than the between condition signal (which in turn doesn't mean that you won't find any differentially expressed genes). More concerning is if the samples cluster, but by something other than the biological groupings - for example by the batch in which they were run. Again this is an indication of poor signal or high noise, but as long as you have a properly randomised design it doesn't mean that the data is unusable.

    Leave a comment:


  • RNAseq data: how to evaluate if the replicates are good or not

    I have two replicates for each sample and would like to downstream differential gene expression analysis. I could do some correlation analysis, either pearson or spearman. I also scatterplot them (examples attached here). Just wonder how I would tell if the replicates are consistent with each other. I mean for the examples I provided here, can I treat them as replicates?

    Thank you very much for any inputs!
    Attached Files

Latest Articles

Collapse

  • seqadmin
    Pathogen Surveillance with Advanced Genomic Tools
    by seqadmin




    The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
    03-24-2025, 11:48 AM
  • seqadmin
    New Genomics Tools and Methods Shared at AGBT 2025
    by seqadmin


    This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

    The Headliner
    The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
    03-03-2025, 01:39 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-20-2025, 05:03 AM
0 responses
49 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-19-2025, 07:27 AM
0 responses
57 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-18-2025, 12:50 PM
0 responses
50 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-03-2025, 01:15 PM
0 responses
201 views
0 reactions
Last Post seqadmin  
Working...