ArticleBMC bioinformatics2009
Inverse Langmuir method for oligonucleotide microarray analysis.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed.
- Variation of RNA Quality and Quantity Are Major Sources of Batch Effects in Microarray Expression Data.Microarrays (Basel, Switzerland) · 2014Article
- Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.Nucleic acids research · 2013Review
- Motif effects in Affymetrix GeneChips seriously affect probe intensities.Nucleic acids research · 2012Article
- Hybridization and amplification rate correction for affymetrix SNP arrays.BMC medical genomics · 2012Article
- From hybridization theory to microarray data analysis: performance evaluation.BMC bioinformatics · 2011Article
- Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model.PloS one · 2010Article
- G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration.BMC bioinformatics · 2010Article
- Linear model for fast background subtraction in oligonucleotide microarrays.Algorithms for molecular biology : AMB · 2009Article
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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAn algorithm for the analysis of Affymetrix Genechips is presented. This algorithm, referred to as the Inverse Langmuir Method (ILM), estimates the binding of transcripts to complementary probes using DNA/RNA hybridization free energies, and the hybridization between partially complementary transcripts in solution using RNA/RNA free energies. The balance between these two competing reactions allows for the translation of background-subtracted intensities into transcript concentrations.
resultsTo validate the ILM, it is applied to publicly available microarray data from a multi-lab comparison study. Here, microarray experiments are performed on samples which deviate only in few genes. The log2 fold change between these two samples, as obtained from RT-PCR experiments, agrees well with the log2 fold change as obtained with the ILM, indicating that the ILM determines changes in the expression level accurately. We also show that the ILM allows for the identification of outlying probes, as it yields independent concentration estimates per probe.
conclusionThe ILM is robust and offers an interesting alternative to purely statistical algorithms for microarray data analysis.
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.