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【数据质控】用Boxplots检查样本间的归一化(normalization)

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licheng 发表于 2016-4-10 18:50:38 | 显示全部楼层 |阅读模式
用Boxplot检查芯片数据是否做了合理normalization
3/13/2014

【Cheng】下图中每一个box代表一个芯片里所有基因表达值的分布。如果没有normalize或没做好,比较两个芯片时会有许多假阳性的差异表达基因。做normalization的假设是:
  • 在两个芯片(样本)之间,只有少部分基因有差异表达,但所有基因的表达值的分布没有太大变化。
  • Normalization之前的数据中,两个芯片分布的差异是由于mRNA总量不同,或者试剂和芯片扫描仪造成的对所有基因类似的系统差异(如让所有基因的表达值升高)。

2012.10.11     Use boxplots to inspect microarray data before and after normalization

Figure from: http://www.biolsci.org/v04p0223.htm



figure.jpg


"Box plots of expression data before and after normalization. The quantile normalization algorithms[25] were used to adjust the values of the background-subtracted mean pixel intensities of each and every set of 800 genes that were selected from the hMitChip3 triplicate microarray experiments hybridized with PTSD and control prefrontal cortex RNA samples as described previously[24]. In contrast to the pre-normalization boxplots (top panel), the post-normalized boxplots distribute in the same intervals with the same density center, indicating successful adjustment of data. The post-normalized data were used for clustering analysis. S-E: Sample and independent microarray experiment."

8/4/09: Lowess normalization

See these links:

plot in page 10:
http://www.bioconductor.org/packages/release/bioc/vignettes/marray/inst/doc/marrayNorm.pdf


http://www.improvedoutcomes.com/docs/WebSiteDocs/PreProcessing/Normalization/Two_Color_Datasets/Overview_of_Lowess_Normalization.htm


and use this BioConductor package:

http://bioconductor.org/packages/2.4/bioc/html/marray.html


M-A normalization normalizes the log ratios between the two arrays. To get raw log values of the array 2, use (array 1 + normalized log ratios).

Cheng



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