Literature DB >> 16935927

An application for assessing quality of RNA hybridized to Affymetrix GeneChips.

Kellie J Archer1, Tobias Guennel.   

Abstract

UNLABELLED: This paper describes a stand-alone application for estimating the 3' to 5' ratio by fitting a mixed effects model to the interior pixel intensities of perfect match probes for selected control probe sets from an Affymetrix *.DAT file. The effectiveness of this method was demonstrated previously by an application of the method to two microarray datasets for which external verification of RNA quality was known. This application provides a more objective assessment of sample quality in that both a point estimate and 95% confidence interval about the 3' to 5' ratio are provided. AVAILABILITY: The software and installation instructions are freely available for download at http://www.people.vcu.edu/~kjarcher/Research/Data.htm

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Year:  2006        PMID： 16935927     DOI： 10.1093/bioinformatics/btl459

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  8 in total

1.  Pretransplant transcriptome profiles identify among kidneys with delayed graft function those with poorer quality and outcome.

Authors:  Valeria R Mas; Mariano J Scian; Kellie J Archer; Jihee L Suh; Krystle G David; Qing Ren; Todd W B Gehr; Anne L King; Marc P Posner; Thomas F Mueller; Daniel G Maluf
Journal:  Mol Med       Date:  2011-09-06       Impact factor: 6.354

2.  Distinctive gene expression profiles characterize donor biopsies from HCV-positive kidney donors.

Authors:  Valeria R Mas; Kellie J Archer; Lacey Suh; Mariano Scian; Marc P Posner; Daniel G Maluf
Journal:  Transplantation       Date:  2010-12-15       Impact factor: 4.939

3.  Gene expression changes are associated with loss of kidney graft function and interstitial fibrosis and tubular atrophy: diagnosis versus prediction.

Authors:  Mariano J Scian; Daniel G Maluf; Kellie J Archer; Jihee L Suh; David Massey; Ryan C Fassnacht; Benjamin Whitehill; Amit Sharma; Anne King; Todd Gehr; Adrian Cotterell; Marc P Posner; Valeria Mas
Journal:  Transplantation       Date:  2011-03-27       Impact factor: 4.939

Review 4.  Molecular Markers of Kidney Transplantation Outcome: Current Omics Tools and Future Developments.

Authors:  Maryne Lepoittevin; Thomas Kerforne; Luc Pellerin; Thierry Hauet; Raphael Thuillier
Journal:  Int J Mol Sci       Date:  2022-06-05       Impact factor: 6.208

5.  Quality assessment of microarray data in a multicenter study.

Authors:  Kellie J Archer; Valeria R Mas; Thomas R O'Brien; Ruth Pfeiffer; Nicole L Lum; Robert A Fisher
Journal:  Diagn Mol Pathol       Date:  2009-03

6.  Effects of aging and anatomic location on gene expression in human retina.

Authors:  Hui Cai; Mark A Fields; Risa Hoshino; Lucian V Del Priore
Journal:  Front Aging Neurosci       Date:  2012-05-31       Impact factor: 5.750

7.  Estimating RNA-quality using GeneChip microarrays.

Authors:  Mario Fasold; Hans Binder
Journal:  BMC Genomics       Date:  2012-05-14       Impact factor: 3.969

Review 8.  Microarray experiments and factors which affect their reliability.

Authors:  Roman Jaksik; Marta Iwanaszko; Joanna Rzeszowska-Wolny; Marek Kimmel
Journal:  Biol Direct       Date:  2015-09-03       Impact factor: 4.540
  8 in total

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