Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Micro-array: Huex 1st v2

    Hello,

    This is first time I'm dealing with Micro-array data. I've affymetrix human exon arrays. Cases and control in total are 223.
    I tried few things but kind of lost in between.

    I perform rma at probe level and at core level. But the output matrix is same in both the cases is same.
    22,000 rows (one per probe) and column count is 223. I'm unable to understand why is that and how?

    Default:
    Code:
    celFiles <- list.celfiles("../CEL")
    rawData <- read.celfiles(celFiles)
    
    geneSummaries <- rma(rawData)
    PDmatrixRMA<-exprs(geneSummaries)
    getexpression_core<-as.data.frame(as.ffdf(PDmatrixRMA_core))
    write.table(getexpression_core, "PD_RMAnormalized.txt")
    Core level:
    Code:
    celFiles <- list.celfiles("../CEL")
    rawData <- read.celfiles(celFiles)
    
    geneSummaries <- rma(rawData, target="core")
    PDmatrixRMA_core<-exprs(geneSummaries)
    getexpression_core<-as.data.frame(as.ffdf(PDmatrixRMA_core))
    write.table(getexpression_core, "PD_RMAnormalized_core.txt")
    Dimensions for PD_RMAnormalized.txt and PD_RMAnormalized_core.txt are same.

    I'm assming that RMA by default normalizes at probe level.

    ?rma doesn't show me what's the default method it applies.

    other attached packages:
    [1] pd.huex.1.0.st.v2_3.14.1 DBI_0.8 RSQLite_2.1.0
    [4] ff_2.2-13 bit_1.1-12 oligo_1.42.0
    [7] Biostrings_2.46.0 XVector_0.18.0 IRanges_2.12.0
    [10] S4Vectors_0.16.0 Biobase_2.38.0 oligoClasses_1.40.0
    [13] BiocGenerics_0.24.0 dplyr_0.7.4 stringr_1.3.0

    loaded via a namespace (and not attached):
    [1] Rcpp_0.12.16 BiocInstaller_1.28.0
    [3] pillar_1.2.1 compiler_3.4.2
    [5] GenomeInfoDb_1.14.0 bindr_0.1.1
    [7] bitops_1.0-6 iterators_1.0.9
    [9] tools_3.4.2 zlibbioc_1.24.0
    [11] digest_0.6.15 memoise_1.1.0
    [13] preprocessCore_1.40.0 tibble_1.4.2
    [15] lattice_0.20-35 pkgconfig_2.0.1
    [17] rlang_0.2.0 Matrix_1.2-12
    [19] foreach_1.4.4 DelayedArray_0.4.1
    [21] bindrcpp_0.2.2 GenomeInfoDbData_1.0.0
    [23] affxparser_1.50.0 bit64_0.9-7
    [25] grid_3.4.2 glue_1.2.0
    [27] R6_2.2.2 blob_1.1.1
    [29] magrittr_1.5 splines_3.4.2
    [31] codetools_0.2-15 matrixStats_0.53.1
    [33] GenomicRanges_1.30.3 assertthat_0.2.0
    [35] SummarizedExperiment_1.8.1 stringi_1.1.7
    [37] RCurl_1.95-4.10 affyio_1.48.0
    Bioinformaticscally calm

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
23 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
200 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 08:54 AM
0 responses
209 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-02-2024, 03:00 PM
0 responses
192 views
0 likes
Last Post seqadmin  
Working...
X