Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates

doi:10.1186/1471-2164-8-153

BMC Genomics

Volume 8

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Liu F
Jenssen TK
Trimarchi J
Punzo C
Cepko CL
Ohno-Machado L
Hovig E
Patrick Kuo W

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Jenssen TK
Trimarchi J
Punzo C
Cepko CL
Ohno-Machado L
Hovig E
Patrick Kuo W
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Research article

Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates

Fang Liu¹^,3 , Tor-Kristian Jenssen³ , Jeff Trimarchi⁴ , Claudio Punzo⁴ , Connie L Cepko⁴^,5 , Lucila Ohno-Machado⁶ , Eivind Hovig¹^,2 and Winston Patrick Kuo⁶^,7^,8

¹Department of Tumor Biology, Rikshopitalet-Radiumhospitalet Medical Center, Montebello, NO-0310 Oslo, Norway

²Department of Medical Informatics, Rikshopitalet-Radiumhospitalet Medical Center, Montebello, NO-0310 Oslo, Norway

³PubGene AS, Vinderen, NO-0319 Oslo, Norway

⁴Department of Genetics, Harvard Medical School, Boston, MA, USA

⁵Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA

⁶Decision Systems Group, Brigham and Women's Hospital, Boston, MA, USA

⁷Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA

⁸Department of Organismic and Evolutionary Biology/Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA

author email corresponding author email

BMC Genomics 2007, 8:153doi:10.1186/1471-2164-8-153


Published:	7 June 2007

Additional files

Additional file 1:

Evaluation of intra-platform and inter-platform data consistency (Affymetrix, Amersham, Mergen, ABI). This file shows the CVs and correlation coefficients of both the within-platform data set and among the across-platform data.

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Additional file 2:

CAT (Correspondence At the Top) plots,. The CAT plots show cross-platform data correspondence when using one platform as the reference.

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Additional file 3:

List of GO terms derived from GSEA (Gene Set Enrichment Analysis). This file provides a list of GO terms which are shown as being variable between the two biological replicate pools used in our study.

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Additional file 4:

Illumina BeadArray^®Experimental Protocols. This is the detailed description of experimental protocols for Illumina BeadArray^®chip.

Format: PDF Size: 134KB Download file

This file can be viewed with: Adobe Acrobat Reader