Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Performing eQTL on FPKMs?

    We are planning to perform an eQTL analysis where the genotype input, at this time, will only be from a previous genotyping microarray run.

    In this case, would it still be appropriate for us to run the analysis using a traditional QTL algorithm (R/qtl method em) and using Cufflinks FPKM as phenotype input? I see many papers talking about doing analysis this way using microarray data, but not so much using RNA-seq data, and are not completely sure if the results are directly comparable...

    Thanks for the help!

  • #2
    Well, at the very minimum, you should log-transform your FPKM values. But why don't you have a look at some RNA-Seq eQTL papers to see how they do it?

    Comment


    • #3
      Originally posted by Simon Anders View Post
      Well, at the very minimum, you should log-transform your FPKM values. But why don't you have a look at some RNA-Seq eQTL papers to see how they do it?
      Hi Simon,

      Not that I haven't did literature search before, but the answer is inconclusive. While I can generally conclude microarray methods can be applied to FPKMs (or in some cases raw counts), but the transformations used in different papers are different-- some papers would just do a simple log transform as you said, but some (like Pritchard) would do a qqnorm, then a PCA to remove 16 unknown factors, then qqnorm again...

      I'm running a log transform to see what happens. Using raw Cufflinks FPKM gave unsatisfactory results.

      Cheers,

      John

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Current Approaches to Protein Sequencing
        by seqadmin


        Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
        04-04-2024, 04:25 PM
      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 12:08 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      17 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 09:21 AM
      0 responses
      14 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-04-2024, 09:00 AM
      0 responses
      43 views
      0 likes
      Last Post seqadmin  
      Working...
      X