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SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips.
Maksimovic J, Gordon L, Oshlack A. Maksimovic J, et al. Among authors: oshlack a. Genome Biol. 2012 Jun 15;13(6):R44. doi: 10.1186/gb-2012-13-6-r44. Genome Biol. 2012. PMID: 22703947 Free PMC article.
Here we present Subset-quantile Within Array Normalization (SWAN), a new method that substantially improves the results from this platform by reducing technical variation within and between arrays. ...
Here we present Subset-quantile Within Array Normalization (SWAN), a new method that substantially improves the results from this pla …
Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes.
Oshlack A, Emslie D, Corcoran LM, Smyth GK. Oshlack A, et al. Genome Biol. 2007;8(1):R2. doi: 10.1186/gb-2007-8-1-r2. Genome Biol. 2007. PMID: 17204140 Free PMC article.
Here we outline a normalization method for use when the assumptions of lowess normalization fail. Specifically, this can occur when specialized boutique arrays are constructed that contain a subset of genes selected to test particular biological functions....
Here we outline a normalization method for use when the assumptions of lowess normalization fail. Specifically, this can occur when s …
Using DNA microarrays to study gene expression in closely related species.
Oshlack A, Chabot AE, Smyth GK, Gilad Y. Oshlack A, et al. Bioinformatics. 2007 May 15;23(10):1235-42. doi: 10.1093/bioinformatics/btm111. Epub 2007 Mar 23. Bioinformatics. 2007. PMID: 17384014
DNA microarrays are a key technology that enables these studies. Currently, however, microarrays are only available for a small number of species. ...We also demonstrate that within-species expression differences can be estimated using a microarray for a
DNA microarrays are a key technology that enables these studies. Currently, however, microarrays are only available for a smal …
Transcript length bias in RNA-seq data confounds systems biology.
Oshlack A, Wakefield MJ. Oshlack A, et al. Biol Direct. 2009 Apr 16;4:14. doi: 10.1186/1745-6150-4-14. Biol Direct. 2009. PMID: 19371405 Free PMC article.
As yet, a rigorous analysis methodology has not been developed and we are still in the stages of exploring the features of the data. ...CONCLUSION: Transcript length bias for calling differentially expressed genes is a general feature of current protocols for RNA-se …
As yet, a rigorous analysis methodology has not been developed and we are still in the stages of exploring the features of the data. …
Gene ontology analysis for RNA-seq: accounting for selection bias.
Young MD, Wakefield MJ, Smyth GK, Oshlack A. Young MD, et al. Among authors: oshlack a. Genome Biol. 2010;11(2):R14. doi: 10.1186/gb-2010-11-2-r14. Epub 2010 Feb 4. Genome Biol. 2010. PMID: 20132535 Free PMC article.
Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology....
Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more co …
A scaling normalization method for differential expression analysis of RNA-seq data.
Robinson MD, Oshlack A. Robinson MD, et al. Among authors: oshlack a. Genome Biol. 2010;11(3):R25. doi: 10.1186/gb-2010-11-3-r25. Epub 2010 Mar 2. Genome Biol. 2010. PMID: 20196867 Free PMC article.
We outline a simple and effective method for performing normalization and show dramatically improved results for inferring differential expression in simulated and publicly available data sets....
We outline a simple and effective method for performing normalization and show dramatically improved results for inferring differenti …
Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips.
Shi W, Oshlack A, Smyth GK. Shi W, et al. Among authors: oshlack a. Nucleic Acids Res. 2010 Dec;38(22):e204. doi: 10.1093/nar/gkq871. Epub 2010 Oct 6. Nucleic Acids Res. 2010. PMID: 20929874 Free PMC article.
The strategies include a popular variance stabilizing transformation and model-based background corrections that either use or ignore the control probes. ...The use of control probes as part of the background correction and normalization strategy is shown to achieve the lo …
The strategies include a popular variance stabilizing transformation and model-based background corrections that either use or ignore …
From RNA-seq reads to differential expression results.
Oshlack A, Robinson MD, Young MD. Oshlack A, et al. Genome Biol. 2010;11(12):220. doi: 10.1186/gb-2010-11-12-220. Epub 2010 Dec 22. Genome Biol. 2010. PMID: 21176179 Free PMC article. Review.
ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity.
Young MD, Willson TA, Wakefield MJ, Trounson E, Hilton DJ, Blewitt ME, Oshlack A, Majewski IJ. Young MD, et al. Among authors: oshlack a. Nucleic Acids Res. 2011 Sep 1;39(17):7415-27. doi: 10.1093/nar/gkr416. Epub 2011 Jun 7. Nucleic Acids Res. 2011. PMID: 21652639 Free PMC article.
First, a broad domain of H3K27me3 enrichment across the body of genes corresponds to the canonical view of H3K27me3 as inhibitory to transcription. ...Finally and most surprisingly, we identified an enrichment profile with a peak in the promoter of genes that is ass …
First, a broad domain of H3K27me3 enrichment across the body of genes corresponds to the canonical view of H3K27me3 as inhibitory to …
Bpipe: a tool for running and managing bioinformatics pipelines.
Sadedin SP, Pope B, Oshlack A. Sadedin SP, et al. Among authors: oshlack a. Bioinformatics. 2012 Jun 1;28(11):1525-6. doi: 10.1093/bioinformatics/bts167. Epub 2012 Apr 12. Bioinformatics. 2012. PMID: 22500002
SUMMARY: Bpipe is a simple, dedicated programming language for defining and executing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflo …
SUMMARY: Bpipe is a simple, dedicated programming language for defining and executing bioinformatics pipelines. It specializes in ena …
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