a question about input agilent single-channel data to R and analyze
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@nkucorluce-6852
Last seen 6.9 years ago
Turkey

Dear bioconductor,

I'm a PHd student and started to study in bioinformatics. I have some data to analyze with bioconductor. But I don't known how to start analyze the data. Waiting for your suggestions. How should I follow  a path.

Here is a sample of agilent data.

Thanks for your reading my message.

Best wishes,

TYPE    text    text    text    integer    text    float    float    text    integer    text    text    integer    integer    integer    integer    float    float    float    float    float    float    text    text    text    text    text    text    text    text    text    text    text    integer    integer    integer
FEPARAMS    Protocol_Name    Protocol_date    Scan_ScannerName    Scan_NumChannels    Scan_Date    Scan_MicronsPerPixelX    Scan_MicronsPerPixelY    Scan_OriginalGUID    Scan_NumScanPass    Grid_Name    Grid_Date    Grid_NumSubGridRows    Grid_NumSubGridCols    Grid_NumRows    Grid_NumCols    Grid_RowSpacing    Grid_ColSpacing    Grid_OffsetX    Grid_OffsetY    Grid_NomSpotWidth    Grid_NomSpotHeight    Grid_GenomicBuild    FeatureExtractor_Barcode    FeatureExtractor_Sample    FeatureExtractor_ScanFileName    FeatureExtractor_ArrayName    FeatureExtractor_ScanFileGUID    FeatureExtractor_DesignFileName    FeatureExtractor_ExtractionTime    FeatureExtractor_UserName    FeatureExtractor_ComputerName    FeatureExtractor_Version    FeatureExtractor_IsXDRExtraction    FeatureExtractor_ColorMode    FeatureExtractor_QCReportType
DATA    miRNA_107_Sep09 (Read Only)    29-Sep-2009 12:14    Agilent Technologies Scanner G2505C US10133796    1    07-09-2014 15:59:08    3    3    9fa6daa0-31fc-4d0e-8222-a4019c10f815    1    046064_D_F_20121223    23-Dec-2012 00:00    1    1    384    164    36.6617    31.745    0    18.3309    30    30    hg19:GRCh37:Feb2009    254606412513_1_2        D:\ScanData\Tukuruk\140709\80\\US10133796_254606412513_S01.tif    US10133796_254606412513_S01    0da40ae4-2ec3-4ef3-92c7-01db11da452f    046064_D_F_20121223.xml    09-Jul-2014 16:02:12    Administrator    DEMO    10.7.3.1    0    0    2
*
TYPE    float    float    float    integer    integer    float    float    float    integer    float    float    float    integer    float    float    integer    integer    integer    integer    integer    float    float    float    integer    float    float    float    float    float    integer    integer    float    float    float    float    float    integer    float    float    float    float    integer    float    float    float    float    float    integer    float    float    float    float    float    float    float    integer    float    integer    float    float    float    float    integer    float    float    text    float    float    float    float    float    float    float    float    integer    integer    integer    integer    float    float    float    integer    float    integer    text    float    float    integer    float    float    float    float    float    float    boolean    float    float    boolean    float    boolean    float    boolean    float    boolean    float    boolean    float    boolean    float    boolean    float    boolean

...
*
TYPE    integer    integer    integer    integer    integer    text    text    float    float    float    float    float    float    float    boolean    boolean    boolean    boolean    boolean    boolean    float    boolean    boolean    float    float    float    float    float    float    boolean
FEATURES    FeatureNum    Row    Col    SubTypeMask    ControlType    ProbeName    SystematicName    PositionX    PositionY    gProcessedSignal    gProcessedSigError    gMedianSignal    gBGMedianSignal    gBGPixSDev    gIsSaturated    gIsFeatNonUnifOL    gIsBGNonUnifOL    gIsFeatPopnOL    gIsBGPopnOL    IsManualFlag    gBGSubSignal    gIsPosAndSignif    gIsWellAboveBG    SpotExtentX    gBGMeanSignal    gTotalProbeSignal    gTotalProbeError    gTotalGeneSignal    gTotalGeneError    gIsGeneDetected
DATA    1    1    1    0    1    miRNABrightCorner30    miRNABrightCorner30    5889.97    465.588    1.865756e+002    1.877887e+001    223.5    17    5.484242e+000    0    0    0    1    0    0    186.576    1    1    26.8687    17.0277    993.25    100.829    993.25    100.829    1
DATA    2    1    2    0    1    Blank    Blank    5911    465.5    -1.488655e+001    2.131084e+000    18    17    5.459987e+000    0    0    0    0    0    0    -14.8866    0    0    30    17.012    -101.775    13.4022    0.1    1    0
DATA    3    1    3    0    1    Blank    Blank    5932    465.5    -1.596166e+001    2.131084e+000    16    17    5.502248e+000    0    0    0    0    0    0    -15.9617    0    0    30    17.0844    -101.775    13.4022    0.1    1    0
DATA    4    1    4    0    1    Blank    Blank    5953.22    465.478    -1.555838e+001    2.131084e+000    17    17    5.488457e+000    0    0    0    0    0    0    -15.5584    0    0    27.0811    17.1062    -101.775    13.4022    0.1    1    0

full data

Agilent microarray • 1.4k views
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@merienne-nicolas-6729
Last seen 3.8 years ago
Switzerland

Hello,

 

I think the package AgiMicroRna developped by Pedro Lopez-Romero is a good starting for Agilent miRNA microarray analysis. The vignette is clear and will guide you along the analysis. I tried it for a project and obtained good results. However, I am not bioinformatician, it is just my own experience with this package and maybe other tools/methods should be better. In addition, you should read articles concerning normalization methods for microarray, there are a lot (quantile, RMA,...) with their own advantages/disadvantages depending on the type of data you are using.

 

I hope this will be usefull for you.

Best,

Nicolas

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Thanks a lot.

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@gordon-smyth
Last seen 9 hours ago
WEHI, Melbourne, Australia

The file format you show is the standard format written by Agilent's Feature Extraction software. The limma User's Guide explains how to read such data in Section 4.5 "Reading Single-Channel Agilent Intensity Data", see:

 http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf

A complete start-to-finish worked example of reading and analyzing such data is given in the case study in Section 17.4.

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Thank you very much.

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