Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how to normalize RNA-seq with microarray data?

    hi,

    I have some gene expression data measured by RNA-seq or microarray. but RNA-seq data gene expression level generally higher than microarray.How should I normalize the data to find the different expression gene?

    Thanks in advance
    Any help would be appreciated.

  • #2
    Most of the methods in use aren't meant for this in any way. However, you might be able to use WGCNA, which can work on microarrays or RNAseq, just include the technology type as a factor. Similarly, perhaps limma will work OK (again, include the technology type as a batch effect).

    This assumes, of course, that your groups are not separated according the the techonology (i,e, group A has microarray data and group B RNAseq any you want to find DE genes between the two). That's unlikely to work well regardless of the method.

    Comment


    • #3
      If I want to compare my RNA-seq with publicly available microarray datasets, I tend to work with fold expression instead of actual expression values. That should make the direct comparison legit.

      Comment


      • #4
        That won't make the comparisons legitimate if you actually plan on looking for DE genes between the technologies. The signals on a microarray are independent, whereas read counts are competitive, so they have different distributions. You can try to normalize that away but I'd be hesitant to believe the results without having first done a validation experiment with known results (e.g. running the same samples on both platforms and ensuring that the resulting profiles are the close enough and there are effectively no DE genes in a comparison).

        Comment


        • #5
          Originally posted by DonDolowy View Post
          If I want to compare my RNA-seq with publicly available microarray datasets, I tend to work with fold expression instead of actual expression values. That should make the direct comparison legit.

          What is the meaning of fold expression?

          Comment

          Latest Articles

          Collapse

          • 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
          • seqadmin
            The Impact of AI in Genomic Medicine
            by seqadmin



            Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
            02-26-2024, 02:07 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 03-14-2024, 06:13 AM
          0 responses
          33 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-08-2024, 08:03 AM
          0 responses
          72 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-07-2024, 08:13 AM
          0 responses
          81 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-06-2024, 09:51 AM
          0 responses
          68 views
          0 likes
          Last Post seqadmin  
          Working...
          X