ArticleBMC bioinformatics2010
Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 27 citations in OpenAlex.
- An integrative analysis to reveal that CLEC2B and ferroptosis may bridge the gap between psoriatic arthritis and cancer development.Scientific reports · 2022Article
- A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression.Life (Basel, Switzerland) · 2021Article
- The orphan nuclear receptor Nr4a1 mediates perinatal neuroinflammation in a murine model of preterm labor.Cell death & disease · 2020Article
- Comparative transcriptomics indicate changes in cell wall organization and stress response in seedlings during spaceflight.American journal of botany · 2017Article
- Article
- Analysis of the protein-protein interaction networks of differentially expressed genes in pulmonary embolism.Molecular medicine reports · 2015Article
- Identification of differential splicing genes in gliomas using exon expression profiling.Molecular medicine reports · 2015Article
- Article
- Transcriptomic signatures of peroxisome proliferator-activated receptor α (PPARα) in different mouse liver models identify novel aspects of its biology.BMC genomics · 2014Article
- Patterns of gene expression associated with recovery and injury in heat-stressed rats.BMC genomics · 2014Article
- Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome.Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologica · 2014Article
- Article
- Cross-species gene expression analysis of species specific differences in the preclinical assessment of pharmaceutical compounds.PloS one · 2014Article
- Article
- Treatment of mouse liver slices with cholestatic hepatotoxicants results in down-regulation of Fxr and its target genes.BMC medical genomics · 2013Article
- HDM2 promotes WIP1-mediated medulloblastoma growth.Neuro-oncology · 2012Article
- Hypoxia-induced alternative splicing in endothelial cells.PloS one · 2012Article
- Implementation of exon arrays: alternative splicing during T-cell proliferation as determined by whole genome analysis.BMC genomics · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlternative 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.
resultsIn 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.
conclusionWe 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.