AffyRNADegradation: Control and correction of RNA quality effects in GeneChip expression data

Bioinformatics

Volumn 29, Issue 1, 2013, Pages 129-131

  Fasold, Mario ^a   Binder, Hans ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION PROFILING; HUMAN; METABOLISM; RNA STABILITY; STANDARD;

GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA STABILITY; RNA, MESSENGER; SOFTWARE;

EID: 84871806112     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts629     Document Type: Article

References (8)

1. Archer, K.J. et al. (2006) Assessing quality of hybridized RNA in Affymetrix GeneChip experiments using mixed-effects models. Biostatistics, 7, 198-212.
2. Binder, H. (2006) Thermodynamics of competitive surface adsorption on DNA microarrays-theoretical aspects. J. Phys. Cond. Mat., 18, S491-S523.
3. Fasold, M. and Binder, H. (2012) Estimating RNA-quality using GeneChip micro-arrays. BMC Genomics, 13, 186.
4. Fleige, S. and Pfaffl, M.W. (2006) RNA integrity and the effect on the real-time qRT-PCR performance. Mol. Aspects Med., 27, 126-139.
5. Gautier, L. et al. (2004) affy-Analysis of Affymetrix GeneChip data at the probe level. Bioinformatics, 20, 307-315. (Pubitemid 38262761)
6. Ma, C. et al. (2006) In vitro transcription amplification and labeling methods contribute to the variability of gene expression profiling with DNA microarrays. J. Mol. Diagn., 8, 183-192. (Pubitemid 43811241)
7. Schroeder, A. et al. (2006) The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol. Biol., 7, 3.
8. Upton, G.J. et al. (2009) On the causes of outliers in Affymetrix GeneChip data. Brief. Funct. Genomic. Proteomic., 8, 199-212.