Högskolan i Skövde

his.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • apa-cv
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Normalization of microRNA expression levels in Quantitative RT-PCR arrays
University of Skövde, School of Life Sciences.
2010 (English)Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
Abstract [en]

Background: Real-time quantitative Reverse Transcriptase Polymerase Chain Reaction (qRT-PCR) is recently used for characterization and expression analysis of miRNAs. The data from such experiments need effective analysis methods to produce reliable and high-quality data. For the miRNA prostate cancer qRT-PCR data used in this study, standard housekeeping normalization method fails due to non-stability of endogenous controls used. Therefore, identifying appropriate normalization method(s) for data analysis based on other data driven principles is an important aspect of this study.

Results: In this study, different normalization methods were tested, which are available in the R packages Affy and qpcrNorm for normalization of the raw data. These methods reduce the technical variation and represent robust alternatives to the standard housekeeping normalization method. The performance of different normalization methods was evaluated statistically and compared against each other as well as with the standard housekeeping normalization method. The results suggest that qpcrNorm Quantile normalization method performs best for all methods tested.

Conclusions: The qpcrNorm Quantile normalization method outperforms the other normalization methods and standard housekeeping normalization method, thus proving the hypothesis of the study. The data driven methods used in this study can be applied as standard procedures in cases where endogenous controls are not stable.

Place, publisher, year, edition, pages
2010. , p. 30
Keywords [en]
Normalization, MicroRNA, Quantile, qRT-PCR
National Category
Bioinformatics and Computational Biology
Identifiers
URN: urn:nbn:se:his:diva-4133OAI: oai:DiVA.org:his-4133DiVA, id: diva2:324414
Presentation
2010-05-19, P201, Portalen, Skövde, 14:00 (English)
Uppsok
Medicine
Supervisors
Examiners
Available from: 2010-06-16 Created: 2010-06-15 Last updated: 2025-02-07Bibliographically approved

Open Access in DiVA

Ameya_Thesis(944 kB)422 downloads
File information
File name FULLTEXT01.pdfFile size 944 kBChecksum SHA-512
03c0696121a6f5eafaa08c83dec910a635b3c2bb846c4d5c64b25576561cb603e57503e1a675daf70d2f6e298a758c694771372e8883ec3eba74b867248ee2e9
Type fulltextMimetype application/pdf
fulltext(944 kB)507 downloads
File information
File name FULLTEXT02.pdfFile size 944 kBChecksum SHA-512
03c0696121a6f5eafaa08c83dec910a635b3c2bb846c4d5c64b25576561cb603e57503e1a675daf70d2f6e298a758c694771372e8883ec3eba74b867248ee2e9
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Deo, Ameya
By organisation
School of Life Sciences
Bioinformatics and Computational Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 931 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

urn-nbn

Altmetric score

urn-nbn
Total: 868 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • apa-cv
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf