Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • getting data into DESeq2

    Hi there,
    i've got R version 3.1.0
    DESeq2 version 1.4.5

    I'm trying to get my data into R to create a DESeq object and i've tried following the vignette to work out how I may put my data in instead and I feel like i'm banging my head against a brick wall.

    I've got 3 reps of 6 treatments in my countData file with geneIDs in the first column.

    My experimental design is in a second csv file.

    What i'm missing is the ability to tell DESeq exactly what these two files contain, and then syntax to marry the two together using DESeqDataSetFromMatrix

    Apologies for this entry-level question
    Any tips much appreciated

    Anna


    Here's what i've inputted so far:
    countData <- read.csv ("C:/Documents and Settings/x991064/Desktop/EXPRESSION/sporesVbase.csv", header=T, row.names=1)
    > head(countData)
    C1 C2 C3 W2 W4 W5 PB1 PB2 PB5 RB1 RB2 RB4 TB1
    CPUR_00001.1 0 0 0 0 0 0 0 0 0 0 0 0 1
    CPUR_00002.1 0 0 0 0 0 3 0 0 0 0 0 0 4
    CPUR_00003.1 0 0 0 0 0 1 0 0 0 1 0 0 2
    CPUR_00004.1 0 0 1 3 2 8 0 0 0 0 1 0 4
    CPUR_00005.1 1 0 3 37 25 6 0 0 0 0 0 0 12
    CPUR_00006.1 23 1 67 60 60 146 0 0 0 18 11 6 223
    TB2 TB4 VB1 VB2 VB3
    CPUR_00001.1 1 0 0 0 0
    CPUR_00002.1 1 1 0 2 4
    CPUR_00003.1 1 2 0 1 1
    CPUR_00004.1 1 6 25 29 25
    CPUR_00005.1 0 3 6 6 3
    CPUR_00006.1 93 174 163 251 144
    > colData <- read.csv("C:/Documents and Settings/x991064/Desktop/EXPRESSION/sporesVbaseDesign.csv")
    > head(colData)
    X time location treatment
    1 C1 0 spores C
    2 C2 0 spores C
    3 C3 0 spores C
    4 W2 1 germ W
    5 W4 1 germ W
    6 W5 1 germ W

  • #2
    hi Anna,

    In R, you tell a function which is which by either providing the objects in the order in the help file, or by naming them.

    For more information about a function you can always type ?DESeqDataSetFromMatrix.

    As far as building a DESeqDataSet, in the vignette we have:

    Now that we have a matrix of counts and the column information, we can construct a DESeqDataSet:

    dds <- DESeqDataSetFromMatrix(countData = countData,
    colData = colData,
    design = ~ condition)
    You are ready to go as the countData and colData are in the same order.

    You can see that this is true with:

    all(colnames(countData) == colData$X)

    So you just need to specify the experimental design using an R formula.

    This might be:

    ~ time + location + treatment

    But the design you should specify depends on what your biological question is for this experiment.

    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
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    9 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