affyGG: computational protocols for genetical genomics with Affymetrix arrays

Rudi Alberts; Gonzalo Vera; Ritsert C. Jansen

doi:10.1093/bioinformatics/btm614

affyGG: computational protocols for genetical genomics with Affymetrix arrays

Rudi Alberts, Gonzalo Vera, Ritsert C. Jansen^*

^*Corresponding author voor dit werk

Onderzoeksoutput › Academic › peer review

8 Citaten (Scopus)

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Motivation: Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes.

Results: We present custom software to analyze genetical genomics experiments in human, mouse and other organisms: (i) an R package providing functions for QTL analysis at the individual probe level and (ii) Perl scripts providing custom tracks in the UCSC Genome Browser to check for sequence polymorphisms in probe regions.

Originele taal-2	English
Pagina's (van-tot)	433-434
Aantal pagina's	2
Tijdschrift	Bioinformatics
Volume	24
Nummer van het tijdschrift	3
DOI's	https://doi.org/10.1093/bioinformatics/btm614
Status	Published - 1-feb.-2008

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abstract = "Motivation: Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes.Results: We present custom software to analyze genetical genomics experiments in human, mouse and other organisms: (i) an R package providing functions for QTL analysis at the individual probe level and (ii) Perl scripts providing custom tracks in the UCSC Genome Browser to check for sequence polymorphisms in probe regions.",

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year = "2008",

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AU - Alberts, Rudi

AU - Vera, Gonzalo

AU - Jansen, Ritsert C.

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N2 - Motivation: Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes.Results: We present custom software to analyze genetical genomics experiments in human, mouse and other organisms: (i) an R package providing functions for QTL analysis at the individual probe level and (ii) Perl scripts providing custom tracks in the UCSC Genome Browser to check for sequence polymorphisms in probe regions.

AB - Motivation: Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes.Results: We present custom software to analyze genetical genomics experiments in human, mouse and other organisms: (i) an R package providing functions for QTL analysis at the individual probe level and (ii) Perl scripts providing custom tracks in the UCSC Genome Browser to check for sequence polymorphisms in probe regions.

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DO - 10.1093/bioinformatics/btm614

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JO - Bioinformatics

JF - Bioinformatics

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affyGG: computational protocols for genetical genomics with Affymetrix arrays

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