Header Leaderboard Ad

Collapse

HTseq-count to DEseq2: Need a little help..

Collapse

Announcement

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

  • sindrle
    replied
    No surprise, that worked like a charm!

    Thanks again, Ill try to run DEseq2 now for diff.exp.

    Leave a comment:


  • dpryan
    replied
    Ah, I see what the problem is. colData is is set from SampleTable (it's all but the first 2 columns). However, there's just a single column there and you have two factors in your design. Try the following:

    Code:
    sampleFiles <- list.files(path="/Volumes/timemachine/HTseq_DEseq2",pattern="*.txt")
    status <- factor(c(rep("Healthy",26), rep("Diabetic",22)))
    timepoints = as.factor(c(1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2))
    sampleTable <- data.frame(sampleName = sampleFiles, fileName = sampleFiles, status=status, timepoints=timepoints)
    directory <- c("/Volumes/timemachine/HTseq_DEseq2/")
    des <- formula(~timepoints+status)
    ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= des)
    Something along those lines should work (I always use DESeqDataSetFromMatrix).

    Leave a comment:


  • sindrle
    replied
    For the first post:

    sampleCondition =read.table("/Volumes/timemachine/HTseq_DEseq2/03_SampleCondition.txt", header=TRUE)
    condition = sampleCondition

    03_SampleCondition.txt:

    Condition
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Last edited by sindrle; 10-18-2013, 05:57 AM.

    Leave a comment:


  • sindrle
    replied
    Design = des doen not work:

    ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= des)
    Error in validObject(.Object) :
    invalid class "DESeqDataSet" object: all variables in design formula must be columns in colData

    Leave a comment:


  • sindrle
    replied
    Heres my "sampleTable":
    sampleName fileName Condition
    1 D104.txt D104.txt Diabetic_pre-exercise
    2 D121.txt D121.txt Diabetic_pre-exercise
    3 D153.txt D153.txt Diabetic_pre-exercise
    4 D155.txt D155.txt Diabetic_pre-exercise
    5 D161.txt D161.txt Diabetic_pre-exercise
    6 D162.txt D162.txt Diabetic_pre-exercise
    7 D167.txt D167.txt Diabetic_pre-exercise
    8 D173.txt D173.txt Diabetic_pre-exercise
    9 D176.txt D176.txt Diabetic_pre-exercise
    10 D177.txt D177.txt Diabetic_pre-exercise
    11 D179.txt D179.txt Diabetic_pre-exercise
    12 D204.txt D204.txt Diabetic_post-exercise
    13 D221.txt D221.txt Diabetic_post-exercise
    14 D253.txt D253.txt Diabetic_post-exercise
    15 D255.txt D255.txt Diabetic_post-exercise
    16 D261.txt D261.txt Diabetic_post-exercise
    17 D262.txt D262.txt Diabetic_post-exercise
    18 D267.txt D267.txt Diabetic_post-exercise
    19 D273.txt D273.txt Diabetic_post-exercise
    20 D276.txt D276.txt Diabetic_post-exercise
    21 D277.txt D277.txt Diabetic_post-exercise
    22 D279.txt D279.txt Diabetic_post-exercise
    23 N101.txt N101.txt Healthy_pre-exercise
    24 N108.txt N108.txt Healthy_pre-exercise
    25 N113.txt N113.txt Healthy_pre-exercise
    26 N170.txt N170.txt Healthy_pre-exercise
    27 N171.txt N171.txt Healthy_pre-exercise
    28 N172.txt N172.txt Healthy_pre-exercise
    29 N175.txt N175.txt Healthy_pre-exercise
    30 N181.txt N181.txt Healthy_pre-exercise
    31 N182.txt N182.txt Healthy_pre-exercise
    32 N183.txt N183.txt Healthy_pre-exercise
    33 N186.txt N186.txt Healthy_pre-exercise
    34 N187.txt N187.txt Healthy_pre-exercise
    35 N188.txt N188.txt Healthy_pre-exercise
    36 N201.txt N201.txt Healthy_post-exercise
    37 N208.txt N208.txt Healthy_post-exercise
    38 N213.txt N213.txt Healthy_post-exercise
    39 N270.txt N270.txt Healthy_post-exercise
    40 N271.txt N271.txt Healthy_post-exercise
    41 N272.txt N272.txt Healthy_post-exercise
    42 N275.txt N275.txt Healthy_post-exercise
    43 N281.txt N281.txt Healthy_post-exercise
    44 N282.txt N282.txt Healthy_post-exercise
    45 N283.txt N283.txt Healthy_post-exercise
    46 N286.txt N286.txt Healthy_post-exercise
    47 N287.txt N287.txt Healthy_post-exercise
    48 N288.txt N288.txt Healthy_post-exercise

    Leave a comment:


  • dpryan
    replied
    What are the dimensions of sampleTable and have you tried "design=des" rather than "design=~des"? For your first post, what were the dimensions of condition?

    Leave a comment:


  • sindrle
    replied
    I have also tried this:

    status <- factor(c(rep("Healthy",26), rep("Diabetic",22)))
    timepoints = c(1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2)
    des <- formula(~timepoints+status)
    ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ des)

    Same error..

    Leave a comment:


  • sindrle
    started a topic HTseq-count to DEseq2: Need a little help..

    HTseq-count to DEseq2: Need a little help..

    Hi!
    This is what Ive done:

    sampleFiles <- list.files(path="/Volumes/timemachine/HTseq_DEseq2",pattern="*.txt")
    sampleCondition <- read.table("/Volumes/timemachine/HTseq_DEseq2/03_SampleCondition.txt", header=TRUE)
    sampleTable <- data.frame(sampleName = sampleFiles, fileName = sampleFiles, condition = sampleCondition)
    directory <- c("/Volumes/timemachine/HTseq_DEseq2/")
    ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ condition)


    Im getting an error:

    "Error in validObject(.Object) :
    invalid class "DESeqDataSet" object: all variables in design formula must be columns in colData"
    Last edited by sindrle; 10-18-2013, 03:56 AM.

Latest Articles

Collapse

  • seqadmin
    A Brief Overview and Common Challenges in Single-cell Sequencing Analysis
    by seqadmin


    ​​​​​​The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i...

    01-24-2023, 01:19 PM
  • seqadmin
    Introduction to Single-Cell Sequencing
    by seqadmin
    Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.

    The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes
    ...
    01-09-2023, 03:10 PM

ad_right_rmr

Collapse
Working...
X