Can subtle changes in gene expression be consistently detected with different microarray platforms?

doi:10.1186/1471-2164-9-124

BMC Genomics
Volume 9

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Pedotti P
't Hoen PA
Vreugdenhil E
Schenk GJ
Vossen RH
Ariyurek Y
de Hollander M
Kuiper R
van Ommen GJ
den Dunnen JT
Boer JM
de Menezes RX

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Pedotti P
't Hoen PA
Vreugdenhil E
Schenk GJ
Vossen RH
Ariyurek Y
de Hollander M
Kuiper R
van Ommen GJ
den Dunnen JT
Boer JM
de Menezes RX
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Research article

Can subtle changes in gene expression be consistently detected with different microarray platforms?

Paola Pedotti¹ , Peter AC 't Hoen¹ , Erno Vreugdenhil³ , Geert J Schenk³ , Rolf HAM Vossen² , Yavuz Ariyurek² , Mattias de Hollander¹^,4 , Rowan Kuiper¹^,4 , Gertjan JB van Ommen¹ , Johan T den Dunnen¹^,2 , Judith M Boer¹ and Renée X de Menezes¹^,5

¹Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands

²Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands

³Division of Medical Pharmacology, Leiden/Amsterdam Center for Drug Research, Leiden, The Netherlands

⁴Department of Technology, Study Programme Bioinformatics, Hogeschool Leiden, Leiden, The Netherlands

⁵Pediatric Oncology, Erasmus Medical Center, Rotterdam, The Netherlands

author email corresponding author email

BMC Genomics 2008, 9:124doi:10.1186/1471-2164-9-124


Published:	10 March 2008

Additional files

Additional file 1:

suppl.material.pedotti. contains a more detailed comparison of the performance of AGL and AFF microarrays.

Format: DOC Size: 533KB Download file

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Additional file 2:

table.S1.pedotti. contains a list of the genes selected for the validation with qRT-PCR and its results.

Format: DOC Size: 93KB Download file

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Additional file 3:

table.S2.pedotti. contains the hybridization design for the two color arrays (AGL and LGTC).

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Additional file 4:

all.data.UG. contains the expression data of all the 5 platforms for the subset of genes with overlapping UG identifiers.

Format: TXT Size: 8.7MB Download file