Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays

Yoseph Barash, Elinor Dehan, Meir Krupsky, Wilbur Franklin, Marc Geraci, Nir Friedman, Naftali Kaminski*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

77 Scopus citations


Motivation: Recent years' exponential increase in DNA microarrays experiments has motivated the development of many signal quantitation (SQ) algorithms. These algorithms perform various transformations on the actual measurements aimed to enable researchers to compare readings of different genes quantitatively within one experiment and across separate experiments. However, it is relatively unclear whether there is a 'best' algorithm to quantitate microarray data. The ability to compare and assess such algorithms is crucial for any downstream analysis. In this work, we suggest a methodology for comparing different signal quantitation algorithms for gene expression data. Our aim is to enable researchers to compare the effect of different SQ algorithms on the specific dataset they are dealing with. We combine two kinds of tests to assess the effect of an SQ algorithm in terms of signal to noise ratio. To assess noise, we exploit redundancy within the experimental dataset to test the variability of a given SQ algorithm output. For the effect of the SQ on the signal we evaluate the overabundance of differentially expressed genes using various statistical significance tests. Results: We demonstrate our analysis approach with three SQ algorithms for oligonucleotide microarrays. We compare the results of using the dChip software and the RMAExpress software to the ones obtained by using the standard Affymetrix MAS5 on a dataset containing pairs of repeated hybridizations. Our analysis suggests that dChip is more robust and stable than the MAS5 tools for about 60% of the genes while RMAExpress is able to achieve an even greater improvement in terms of signal to noise, for more than 95% of the genes.

Original languageAmerican English
Pages (from-to)839-846
Number of pages8
Issue number6
StatePublished - 12 Apr 2004

Bibliographical note

Funding Information:
Y.B. was supported by an Eshkol fellowship. N.F. was supported by an Alon fellowship and the Harry & Abe Sherman Senior Lectureship in Computer Science. N.K.’s work was supported in part by the Tel-Aviv Chapter of the Israeli Lung Association. N.K. is also the Dorothy P. and Richard P. Simmons chair of Interstitial Lung Diseases in the University of Pittsburgh.


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