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表达芯片跟mRNA-seq数据比较(一)

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发表于 2016-11-22 14:25:59 | 显示全部楼层 |阅读模式
文章见:http://journals.plos.org/plosone ... ournal.pone.0078644
指定的细胞系是:Human CCR6+ CD4 memory T cell ,测了6个时间点,共12个样本
表达芯片用的是Affymetrix GeneChip HT HG-U133+ PM arrays
测序用的是: Illumina HiSeq™ 2000 platform,PE,All reads were pair-end sequenced with an average insert size of 160 bp, and typical read-length of 90 bp.

芯片情况介绍:41,796 of the 54,714 probe sets were mapped to 20,741 genes, with 10,837 genes having more than one representative probe set.


比较前先把RPKM值和芯片数值归一化:


In summary, RNA-Seq based transcriptome expression was measured as RPKM for 36,004 transcripts, representing 22,300 unique genes. The median RPKM in all 12 samples was 0.49, and 28.6% to 32.5% (average = 30.3%) of genes had RPKM value of 0 in each sample. In order to make the transcriptome profiling comparable between both platforms (RNA-Seq vs. Microarray), the RPKM values were floored at 0.047, followed by log2 transformation. After the transformation, the difference between the median expression and the floored (minimal) expression by RNA-Seq is equal to the difference between the median expression and the minimal expression by microarray.


文章很有趣,值的细看







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