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一个芯片平台的所有测序数据可以总结成一个包

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发表于 2016-11-9 18:12:41 | 显示全部楼层 |阅读模式
本来想搜索一个mouse的芯片表达数据来做例子,无意中发现了这个包Affymoe4302Expr:https://bioconductor.org/package ... ffymoe4302Expr.html
打开才发现这个包其实就是把GEO数据库里面的所有采用了GPL1261这个芯片平台的数据归纳总结了一下而已,共9444个样本,这个平台会测到20630个mouse的基因表达情况。
下面是它的具体介绍!
This data package contains expression values of 20630 genes and 9444 samples measurements fromNCBI GEO obtained using the GPL1261 platform. Gene expression data were preprocessed andnormalized consistently using fRMA. Gene expression values were further standardized using geneexpression barcode approach. Probeset with the largest coefficient of variaction from all probesetsthat corresponds to the same gene is retained, so that each gene uniquely matches to one row in thedatabase. The biological context of each sample was also recorded and manually verified based onthe sample description in GEO. To enhance the reading speed of the dataset, the gene expressionvalue matrix is stored in a hdf5 format using rhdf5 package. The rows of the matrix representssamples and the columns of the matrix represent genes. Notice that all values are 1000 times theactual value so that the values can be stored as integers to minimize file size and reading time. Thepackage is specifically designed to be manipulated by GSCA package so users are not expected toread the expression values by themselves. The sample id, sample type, and experiment id for eachsample in the gene expression compendium are also included in this data package

bioconductor标准安装方法即可:
source("https://bioconductor.org/biocLite.R")
biocLite('Affymoe4302Expr')

这个数据,我目前也不知道可以做什么,但是感觉这样的包好像没什么技术含量!
trying URL 'https://bioconductor.org/packages/3.2/data/experiment/src/contrib/Affymoe4302Expr_1.8.0.tar.gz'
Content type 'application/x-gzip' length 437878173 bytes (417.6 MB)










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