Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Differential expression graphics

    Hello all,

    I wanna do this type of graphic:
    http://www.jimmunol.org/content/172/...0/F1.small.gif or http://www.omicsonline.org/2157-7099...1-101-g005.gif

    but i'm kind noob in this field... what should be the type of my data?

    i have something like this:

    library/condition geneA geneB geneC
    I 2.0 1.6 12.0
    II 13.0 1.4 0.4
    III 17.0 1.3 0.3

    I use percentages... so for example i know that geneA is more expressed in the III condition, etc... right?

    How can i do a graphic like that one above? sorry my poor english.

  • #2
    Hi Chuckytah,

    The images you refer to, are what are called Heat Maps

    For your kind of data, this will have to be done in 2 steps:
    1. Generate clusters using software like Michiel de Hoon's Cluster
    2. With the files generated there you can use Java TreeView to generate the heat maps

    Good luck

    Comment


    • #3
      In R there is fairly an easy to use function called heatmap that will allow you to do this.
      You can play with scales, colours, and formatting.
      Hope this helps.

      Comment


      • #4
        Originally posted by essvee View Post
        In R there is fairly an easy to use function called heatmap that will allow you to do this.
        You can play with scales, colours, and formatting.
        Hope this helps.
        The function is called "heatmap" ? but it there is no need to install a certain package?

        ty

        Comment


        • #5
          Originally posted by vineeth_s View Post
          Hi Chuckytah,

          The images you refer to, are what are called Heat Maps

          For your kind of data, this will have to be done in 2 steps:
          1. Generate clusters using software like Michiel de Hoon's Cluster
          2. With the files generated there you can use Java TreeView to generate the heat maps

          Good luck
          Thanks a lot. I download those programs i will try later

          Comment


          • #6
            Originally posted by Chuckytah View Post
            The function is called "heatmap" ? but it there is no need to install a certain package?

            ty
            I once used one called "image" to generate a 2D heatmap in R-please don't ask me why not "heatmap".

            Comment


            • #7
              Originally posted by Chuckytah View Post
              The function is called "heatmap" ? but it there is no need to install a certain package?

              ty
              I do not believe you need to install any additional packages. It should be included in your standard installation.
              There are a lot of tutorials floating around, I would suggest searching to find the one most relevant to the type of data you are analyzing.
              Hope this helps

              Comment


              • #8
                Originally posted by steven View Post
                I once used one called "image" to generate a 2D heatmap in R-please don't ask me why not "heatmap".
                The difference is that heatmap rearranges the rows and columns of your matrix by clustering and adds dendrograms, and image does not.

                Comment


                • #9
                  Originally posted by Simon Anders View Post
                  The difference is that heatmap rearranges the rows and columns of your matrix by clustering and adds dendrograms, and image does not.
                  Ah, thanks Simon, I did not remember that. Yes, my matrix had to be plotted "as is", so it makes sense indeed.

                  Comment


                  • #10
                    The multi experiment viewer generates heatmaps in one easy step. Those graphics you sent look like they were made in MeV.

                    Comment


                    • #11
                      I know that heatmaps can be made on R, but my R is not working, dunno why, can't install new packages, maybe because of university proxy.

                      I have done one using Matlab, but it is not so well I think...

                      I will try MeV so

                      Comment

                      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
                      8 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, Yesterday, 06:07 PM
                      0 responses
                      8 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, 03-22-2024, 10:03 AM
                      0 responses
                      49 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