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Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays.

Townsend JP - BMC Genomics (2003)

Bottom Line: Multifactorial experimental designs using DNA microarrays are becoming increasingly common, but the extent of the transitivity of cDNA microarray expression measurements across multiple samples has yet to be explored.A strong correlation between direct and transitive inference for significantly differentially expressed genes is demonstrated, using subsets of a dye-swap loop design.In experimental design, opportunities for transitive inference should be exploited, while always ensuring that comparisons of greatest interest comprise direct hybridizations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, CA 94720, USA. townsend@nature.berkeley.edu

ABSTRACT

Background: Multifactorial experimental designs using DNA microarrays are becoming increasingly common, but the extent of the transitivity of cDNA microarray expression measurements across multiple samples has yet to be explored.

Results: A strong correlation between direct and transitive inference for significantly differentially expressed genes is demonstrated, using subsets of a dye-swap loop design.

Conclusions: In experimental design, opportunities for transitive inference should be exploited, while always ensuring that comparisons of greatest interest comprise direct hybridizations.

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Related in: MedlinePlus

Length of ORF, average spot diameter, and the coefficient of variation of gene expression level. The coefficient of variation estimated for a given gene does not depend upon A) the ORF length, or B) the average spot diameter. Error bars are +/- 2 standard errors of the mean. Larger error bars at either extreme are due to smaller sample size in those size classes and do not reflect a greater standard deviation of the measurements.
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Figure 4: Length of ORF, average spot diameter, and the coefficient of variation of gene expression level. The coefficient of variation estimated for a given gene does not depend upon A) the ORF length, or B) the average spot diameter. Error bars are +/- 2 standard errors of the mean. Larger error bars at either extreme are due to smaller sample size in those size classes and do not reflect a greater standard deviation of the measurements.

Mentions: In order to identify the parameters of DNA microarray experiments that contribute to the experimental error variance, Figure 4 relates experimental error variance to characteristics of the reporter spot. One concern is that polymerase chain reaction (PCR) products spotted on slides may have been better or worse for subsequent hybridization depending on open reading frame (ORF) length. Spots might have better signal when the initial Taq polymerase amplification protocol used for all ORFs was optimal for their length, or when GIBCO Elongase was used on longer, reamplified genes. Figure 4A shows that there is no particular effect of length of the ORF on the error variance of the reporter spot. The large standard error bars at the extremes are a consequence of the few ORFs annotated below 200 base pairs or above 4000 base pairs. This result confirms that the PCR and hybridizations performed were equally successful across many different ORF lengths.


Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays.

Townsend JP - BMC Genomics (2003)

Length of ORF, average spot diameter, and the coefficient of variation of gene expression level. The coefficient of variation estimated for a given gene does not depend upon A) the ORF length, or B) the average spot diameter. Error bars are +/- 2 standard errors of the mean. Larger error bars at either extreme are due to smaller sample size in those size classes and do not reflect a greater standard deviation of the measurements.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC239860&req=5

Figure 4: Length of ORF, average spot diameter, and the coefficient of variation of gene expression level. The coefficient of variation estimated for a given gene does not depend upon A) the ORF length, or B) the average spot diameter. Error bars are +/- 2 standard errors of the mean. Larger error bars at either extreme are due to smaller sample size in those size classes and do not reflect a greater standard deviation of the measurements.
Mentions: In order to identify the parameters of DNA microarray experiments that contribute to the experimental error variance, Figure 4 relates experimental error variance to characteristics of the reporter spot. One concern is that polymerase chain reaction (PCR) products spotted on slides may have been better or worse for subsequent hybridization depending on open reading frame (ORF) length. Spots might have better signal when the initial Taq polymerase amplification protocol used for all ORFs was optimal for their length, or when GIBCO Elongase was used on longer, reamplified genes. Figure 4A shows that there is no particular effect of length of the ORF on the error variance of the reporter spot. The large standard error bars at the extremes are a consequence of the few ORFs annotated below 200 base pairs or above 4000 base pairs. This result confirms that the PCR and hybridizations performed were equally successful across many different ORF lengths.

Bottom Line: Multifactorial experimental designs using DNA microarrays are becoming increasingly common, but the extent of the transitivity of cDNA microarray expression measurements across multiple samples has yet to be explored.A strong correlation between direct and transitive inference for significantly differentially expressed genes is demonstrated, using subsets of a dye-swap loop design.In experimental design, opportunities for transitive inference should be exploited, while always ensuring that comparisons of greatest interest comprise direct hybridizations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, CA 94720, USA. townsend@nature.berkeley.edu

ABSTRACT

Background: Multifactorial experimental designs using DNA microarrays are becoming increasingly common, but the extent of the transitivity of cDNA microarray expression measurements across multiple samples has yet to be explored.

Results: A strong correlation between direct and transitive inference for significantly differentially expressed genes is demonstrated, using subsets of a dye-swap loop design.

Conclusions: In experimental design, opportunities for transitive inference should be exploited, while always ensuring that comparisons of greatest interest comprise direct hybridizations.

Show MeSH
Related in: MedlinePlus