+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays



Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays



Bmc Bioinformatics 11: 211



Alternative splicing is an important mechanism that increases protein diversity and functionality in higher eukaryotes. Affymetrix exon arrays are a commercialized platform used to detect alternative splicing on a genome-wide scale. Two probe summarization algorithms, PLIER (Probe Logarithmic Intensity Error) and RMA (Robust Multichip Average), are commonly used to compute gene-level and exon-level expression values. However, a systematic comparison of these two algorithms on their effects on high-level analysis of the arrays has not yet been reported. In this study, we showed that PLIER summarization led to over-estimation of gene-level expression changes, relative to exon-level expression changes, in two-group comparisons. Consequently, it led to detection of substantially more skipped exons on up-regulated genes, as well as substantially more included (i.e., non-skipped) exons on down-regulated genes. In contrast, this bias was not observed for RMA-summarized data. By using a published human tissue dataset, we compared the tissue-specific expression and splicing detected by Affymetrix exon arrays with those detected based on expressed sequence databases. We found the tendency of PLIER was not supported by the expressed sequence data. We showed that the tendency of PLIER in detection of alternative splicing is likely caused by a technical bias in the approach, rather than a biological bias. Moreover, we observed abnormal summarization results when using the PLIER algorithm, indicating that mathematical problems, such as numerical instability, may affect PLIER performance.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 052605011

Download citation: RISBibTeXText

PMID: 20426803

DOI: 10.1186/1471-2105-11-211


Related references

A new summarization method for Affymetrix probe level data. Bioinformatics 22(8): 943-949, 2006

Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor. Briefings in Bioinformatics 15(4): 519-533, 2015

The comparison of different pre- and post-analysis filters for determination of exon-level alternative splicing events using Affymetrix arrays. Journal of Biomolecular Techniques 21(1): 44-53, 2010

Probe selection and expression index computation of Affymetrix Exon Arrays. Plos One 1: E88, 2006

Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays. Bmc Bioinformatics 11: 578, 2011

High correspondence between Affymetrix exon and standard expression arrays. Biotechniques 42(2): 181-185, 2007

Comprehensive analysis of affymetrix exon arrays using BioConductor. Plos Computational Biology 4(2): E6, 2008

Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acids Research 33(22): E193, 2005

A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. Bmc Bioinformatics 8: 132, 2007

A distribution free summarization method for Affymetrix GeneChip (R) arrays. Bioinformatics 23(3): 321-327, 2007

A distribution free summarization method for Affymetrix GeneChip arrays. Bioinformatics 23(3): 321-327, 2006

Gene expression and isoform variation analysis using Affymetrix exon arrays. Bmc Genomics 10(1): 121-0, 2009

Gene expression and isoform variation analysis using Affymetrix Exon Arrays. Bmc Genomics 9: 529, 2008

Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies. Genome Biology 10(7): R77, 2010

fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays. Bioinformatics 28(23): 3153-3154, 2013