Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • DEseq no significant genes

    Hi everyone,

    I'm very new to the world of RNA-seq so forgive me for my lack of knowledge.

    I got some RNA-seq data from my control cells and treated cells, with 3 replicates of each. The company that did the sequencing provided a bunch of BAM files from aligning the data to the mouse genome with TopHat.

    It was suggested to me that I should use DEseq to analysis the data and thanks to the vignette, I've managed it! (i think).

    My current problem is that when I'm looking at the logfold changes, they are all very very small, like less than 0.5 both sides although the adjusted p value suggests that they are significant. The only thing I can think of is that it might be due to variation between the samples which i believe can be identified from the plotPCA function, although I'm not entirely clear how to interpret it. I've attached the output.

    I'm at a bit of a loss on what to do next, is there a way to lower the stringency of the analysis? or should i just look at the 0.5 fold changes?

    Any help would be greatly appreciated.
    Attached Files

Latest Articles

Collapse

  • 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
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X