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SubtitleText | Transformation can be done on samples or on features |
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AnchorName | transform-on |
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The following normalization methods will generate different results depending on whether the transformation was performed on samples or on features:
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SubtitleText | Normalization using Partek’s recommended method |
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AnchorName | recommended-methods-button |
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Normalization Methods
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SubtitleText | Feature distribution statistic information on each sample and across all the samples |
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AnchorName | feature-distribution-statistic |
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Expression signal
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SubtitleText | Box-whisker plot displays expression signal distribution for each sample |
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AnchorName | box-whisker-plot |
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Sample histogram
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SubtitleText | Sample histogram. Mousing over shows detailed information about the interval. This includes sample name, range and frequency of the selected sample. |
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AnchorName | sample-histogram |
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References
- Bolstad BM, Irizarry RA, Astrand M, Speed, TP. A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics. 2003; 19(2): 185-193.
- Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008; 5(7): 621–628.
- Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics. 2010; 11: 94.
- Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010; 11: R25.
- Dillies MA, Rau A, Aubert J et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform. 2013; 14(6): 671-83.
- Wagner GP, Kin K, Lynch VJ. Measurement of mRNA abundance using RNA-seq data. Theory Biosci. 2012; 131(4): 281-5.
- Ritchie ME, Phipson B, Wu D et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015; 43(15):e97.
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