AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data
Motivation: Gene expression experiments aim to accurately quantify thousands of transcripts in parallel. Factors posterior to RNA extraction can, however, impair their accurate representation. RNA degradation and differences in the efficiency of amplification affect raw intensity measurements using...
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| Format: | Online |
| Language: | English |
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Oxford University Press
2013
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530908/ |
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pubmed-35309082012-12-27 AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data Fasold, Mario Binder, Hans Applications Note Motivation: Gene expression experiments aim to accurately quantify thousands of transcripts in parallel. Factors posterior to RNA extraction can, however, impair their accurate representation. RNA degradation and differences in the efficiency of amplification affect raw intensity measurements using Affymetrix expression arrays. The positional intensity decay of specifically hybridized probes along the transcript they intend to interrogate is used to estimate the RNA quality in a sample and to correct probe intensities for the degradation bias. This functionality, for which no previous software solution is available, is implemented in the R/Bioconductor package AffyRNADegradation presented here. Oxford University Press 2013-01 2012-10-24 /pmc/articles/PMC3530908/ /pubmed/23097420 http://dx.doi.org/10.1093/bioinformatics/bts629 Text en © The Author 2012. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Fasold, Mario Binder, Hans |
| spellingShingle |
Fasold, Mario Binder, Hans AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data |
| author_facet |
Fasold, Mario Binder, Hans |
| author_sort |
Fasold, Mario |
| title |
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data |
| title_short |
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data |
| title_full |
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data |
| title_fullStr |
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data |
| title_full_unstemmed |
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data |
| title_sort |
affyrnadegradation: control and correction of rna quality effects in genechip expression data |
| description |
Motivation: Gene expression experiments aim to accurately quantify thousands of transcripts in parallel. Factors posterior to RNA extraction can, however, impair their accurate representation. RNA degradation and differences in the efficiency of amplification affect raw intensity measurements using Affymetrix expression arrays. The positional intensity decay of specifically hybridized probes along the transcript they intend to interrogate is used to estimate the RNA quality in a sample and to correct probe intensities for the degradation bias. This functionality, for which no previous software solution is available, is implemented in the R/Bioconductor package AffyRNADegradation presented here. |
| publisher |
Oxford University Press |
| publishDate |
2013 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530908/ |
| _version_ |
1611942887334871040 |