Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • chayan
    replied
    Originally posted by southan View Post
    You can use the Mclust package.

    (http://www.stat.washington.edu/mclust/)

    Change the parameter modelNames to obtain a suitable model (e.g., EII).
    thanks.. but i have never used R also... what i understand from the Mclust manual, if my matrix is like this

    A B C D E
    i 20 30 15 43 87
    ii 12 54 3 76 56
    iii 45 78 4 99 54

    i should use the modelName "VII"/"VVV" or other unequal volume or varying volume from the multivariate mixture??

    another thing, how to prepare the input file from the excel to feed into mclust??

    thanks a lot

    Leave a comment:


  • chayan
    replied
    thanks to both of you. As i am going through both the manuals, it will take some time as i am a hardcore biology guy, i want to clear one my query.. my matrix structure is like this
    A B C D E
    i 20 30 15 43 87
    ii 12 54 3 76 56
    iii 45 78 4 99 54

    now i want to cluster this based on the A, B, C, D, E based on the values of i, ii and iii...can i use "beta_diversity.py" from the qiime package..? then dont know basically how to generate to file format required for this as the prior steps are not same...


    thanks

    Leave a comment:


  • southan
    replied
    You can use the Mclust package.

    (http://www.stat.washington.edu/mclust/)

    Change the parameter modelNames to obtain a suitable model (e.g., EII).

    Leave a comment:


  • GenoMax
    replied
    Try MEGA: http://megasoftware.net/

    You should read the manual first to see if this would be appropriate to do with the dataset you have.

    Leave a comment:


  • chayan
    started a topic Clustering a two-D matrix

    Clustering a two-D matrix

    Hii All,

    I have generated a 2-D matrix based on NGS data which has cog scores in one axis (Y-axis) and sample no in other axis. Now i want to cluster this matrix based on the cog scores to find similarity between different sampling points and finally construct a UPGMA tree based on the output. Can any one suggest me a simple way to do this?? I don't have much knowledge about this...

    Thanks for any help in advance...

    Regards

    Chayan

Latest Articles

Collapse

  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    Today, 01:16 PM
  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 07:15 AM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 10:28 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 07:35 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-22-2024, 02:06 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Working...
X