Agi 4 x 44 Preprocess Pedro Lopez - Romero
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چکیده
The Agi4x44PreProcess package has been designed to read Agilent 4 x 44 gene expression arrays data files into R [3] for its pre-processing using other Bioconductor functions. The package needs plain text files exported by the Agilent Feature Extraction 9.1.3.1 (or later version) image analysis software (AFE) [1]. The pre-processing steps implemented in the package are the following: 1.read the target file 2.read the array samples 3.Background correction and Normalization between samples 4.Filtering Probes by Quality Flag 5.Summarizing of Replicated Probes 6.Creating and ExpressionSet object with the processed data The package also contains other utilities that allow the user to explore the architecture of the chip in terms of probe replication and gene replication. Agi4x44PreProcess contains standard graphical utilities to evaluate the quality of the data. These graphics might help the users to decide what sort foreground and background signal, amongst those provided by the AFE, they want to use in their analysis, and what background signal correction and normalization method between samples they want to perform. Finally, Agi4x44PreProcess also generates the files DataSet.gct and Phenotypes.cls that are used by the Gene Set Enrichment Analysis tool (GSEA) [5]. Agi4x44PreProcess employees the corresponding Bioconductor annotation packages (human: ”hgug4112a.db”; mouse: ”mgug4122a.db”) to assign to each probe the ACCNUM, SYMBOL, ENTREZID, DESCRIPTION, GO TERMS AND GO IDS. The annotacion package that is going to be used should be loaded into the R session. In our example we used the hgug4112a.db annotation package. The annotation package can be loaded using library
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Agi 4 x 44 Preprocess Pedro Lopez - Romero April
The Agi4x44PreProcess package has been designed to read Agilent 4 x 44 gene expression arrays data files into R [3] for its pre-processing using other Bioconductor functions. The package needs plain text files exported by the Agilent Feature Extraction 9.1.3.1 (or later version) image analysis software (AFE) [1]. The pre-processing steps implemented in the package are the following: 1.read the ...
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The Agi4x44PreProcess package has been designed to read Agilent 4 x 44 gene expression arrays data files into R [3] for its pre-processing using other Bioconductor functions. The package needs plain text files exported by the Agilent Feature Extraction 9.1.3.1 (or later version) image analysis software (AFE) [1]. The pre-processing steps implemented in the package are the following: 1.read the ...
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تاریخ انتشار 2013