Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • CummeRbund shows 95% NAs for gene lists

    Code:
    cuff_data = readCufflinks(dir=paste0(getwd(),"/../cuffdiff/"), 
                              gtfFile = paste0(getwd(),"/../cuffmerge/merged.gtf"), 
                              genome="hg19", rebuild=F)
    
    #get significant IDs
    diffGeneIDs = getSig(cuff_data, level="genes", alpha=0.05)
    
    diffGenes = getGenes(cuff_data, diffGeneIDs)
    
    featureNames(diffGenes)[1:40,]
    tracking_id gene_short_name
    1 XLOC_000265 CROCC
    2 XLOC_000328 ALPL
    3 XLOC_000443 SYTL1
    4 XLOC_000679 ARTN
    5 XLOC_000938 RNU6-387P
    6 XLOC_001003 FAM73A,RNA5SP21
    7 XLOC_001244 GSTM1,GSTM2
    8 XLOC_001530 ADAMTSL4,AL356356.1,MIR4257
    9 XLOC_001735 FCER1A
    10 XLOC_001988 AXDND1
    11 XLOC_002089 RGS1
    12 XLOC_002211 NFASC,RP11-494K3.2
    13 XLOC_002282 HHAT,KCNH1
    14 XLOC_002522 RYR2
    15 XLOC_002961 PLA2G2A
    16 XLOC_003294 SLC2A1
    17 XLOC_003772 MIR137HG
    18 XLOC_004252 ASH1L,ASH1L-IT1,MIR555
    19 XLOC_004467 RP1-117P20.3,SELE
    20 XLOC_004799 CR1L
    21 XLOC_004802 CD34
    22 XLOC_004843 <NA>
    23 XLOC_005255 <NA>
    24 XLOC_005256 <NA>
    25 XLOC_005257 <NA>
    26 XLOC_005263 <NA>
    27 XLOC_005264 <NA>
    28 XLOC_005265 <NA>
    29 XLOC_005273 <NA>
    30 XLOC_005276 <NA>
    31 XLOC_005277 <NA>
    32 XLOC_005288 <NA>
    33 XLOC_005291 <NA>
    34 XLOC_005292 <NA>
    35 XLOC_005293 <NA>
    36 XLOC_005294 <NA>
    37 XLOC_005322 <NA>
    38 XLOC_005331 <NA>
    39 XLOC_005332 <NA>
    40 XLOC_005333 <NA>
    41 XLOC_005336 <NA>

    Code:
    mean(is.na(as.vector(featureNames(diffGenes)[2])))
    [1] 0.9691279

    This is human data and I have used the same GTF / genome data throughout, so why are so few genes labeled? Only about 3% of the total 6284 differentially expressed genes have labels.
    I have followed the protocol in the nature paper (tophat -> cufflinks -> cuffmerge -> cuffdiff)

    Thanks
    Last edited by bjackson; 05-11-2015, 05:55 PM.

  • #2
    Still looking through this data set. I have 194 named differentially expressed genes. What is the 'normal' amount of differentially expressed genes that you would expect? I know it can vary a lot based on how different the conditions are, but is this in the range of possibility? A lot of the unnamed bits are small chunks or exons. Does this sound like it might be a true result instead of an error in annotation?

    Comment

    Latest Articles

    Collapse

    • 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
    • seqadmin
      Essential Discoveries and Tools in Epitranscriptomics
      by seqadmin




      The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
      04-22-2024, 07:01 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 05-14-2024, 07:03 AM
    0 responses
    19 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-10-2024, 06:35 AM
    0 responses
    43 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-09-2024, 02:46 PM
    0 responses
    53 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-07-2024, 06:57 AM
    0 responses
    42 views
    0 likes
    Last Post seqadmin  
    Working...
    X