| 文章見：http://journals.plos.org/plosone ... ournal.pone.0078644
指定的細(xì)胞系是：Human CCR6+ CD4 memory T cell ，測了6個時間點(diǎn)，共12個樣本
表達(dá)芯片用的是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.?
芯片情況介紹：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值和芯片數(shù)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(xì)看 ? RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays?
http://genome.cshlp.org/content/18/9/1509.full?
Another paper with a variety of comparisons between Affymetrix Exon arrays, custom NimbleGen arrays, and RNA-seq: Griffith, et al. Alternative expression analysis by RNA sequencing. Nature Methods. 2010 Oct;7(10):843-847.
http://www.nature.com/nmeth/journal/v7/n10/full/nmeth.1503.html?
尤其是這個correlation圖，非常重要~~~~
https://www.researchgate.net/fig ... or-RNA-seq-the-LOG2??
第一次看到把圖片描述的比文章還長！~~~~~~~、 ? 文章是：https://genomebiology.biomedcent ... 6/s13059-015-0694-1?
這次是臨床樣本，498個primary neuroblastomas
芯片是：customized 4x44k oligonucleotide microarrays (Agilent Technologies)
測序是：Illumina HiSeq 2000 platform，TruSeq PE cluster Kit v3
數(shù)據(jù)都可以在NCBI里面拿到;
Microarray and RNA-seq data can be accessed from the GEO database (www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE49710 and GSE49711, respectively, which are included in SEQC Project SuperSeries GSE47792. ? ? ? |
