各種平臺的表達晶片跟mRNA-seq資料比較
各種平臺的表達晶片跟mRNA-seq資料比較
文章見：http://journals.plos.org/plosone ... ournal.pone.0078644指定的細胞系是：Human CCR6+ CD4 memory T cell ，測了6個時間點，共12個樣本表達晶片用的是Affymetrix GeneChip HT HG-U13...| 文章見：http://journals.plos.org/plosone ... ournal.pone.0078644 指定的細胞系是：Human CCR6+ CD4 memory T cell ，測了6個時間點，共12個樣本 表達晶片用的是Affymetrix GeneChip HT HG-U133+ PM arrays 測序用的是： 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. 晶片情況介紹：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. 比較前先把RPKM值和晶片數值歸一化： 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，值的細看
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
文章是：https://genomebiology.biomedcent ... 6/s13059-015-0694-1
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