2002
DOI: 10.1093/bioinformatics/18.8.1139
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Abstract: http://matrise.uio.no/marray/marray.html

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Cited by 30 publications
(28 citation statements)
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“…Gene expression was analyzed with CLUSTER (19) by using the average linkage metric. Log-transformed (base 2) median of ratio values were subjected to LOESS normalization by using MARRAY in the R environment (20) and filtered for genes where data were present in 80% of experiments. The resulting data were then analyzed by using the SAM package.…”
Section: Methodsmentioning
confidence: 99%
“…Gene expression was analyzed with CLUSTER (19) by using the average linkage metric. Log-transformed (base 2) median of ratio values were subjected to LOESS normalization by using MARRAY in the R environment (20) and filtered for genes where data were present in 80% of experiments. The resulting data were then analyzed by using the SAM package.…”
Section: Methodsmentioning
confidence: 99%
“…A standardized qualitative assessment of array quality was performed using the Bioconductor arrayQuality package, version 1.4.0 s (Gentleman et al 2004). Spot ratio data were log2 transformed and normalized within each array using print-tip-based loess regression implemented in the Bioconductor MArray package (Wang et al 2002). As all experimental contrasts are represented in the data set at least twice (as dye-flipped replicates) and as many as six times for biological replicates, both within-array and between-array data replication were analyzed for data quality.…”
Section: Microarray Image Analysis and Preprocessingmentioning
confidence: 99%
“…Transcriptional regulation involves multiple transcription factors, kinases, and chromatin modifications (Rohde and Cardenas 2003;Marion et al 2004;Martin et al 2004;Zhao et al 2006). Measurements of mRNA half-lives for all yeast transcripts reveal that the half-lives of the RPGs are strikingly similar to one another, suggesting that this is a regulated property (Wang et al 2002). Moreover, RPGs generally have shorter than average 59 UTRs, which is believed to contribute to their high translational efficiency, and longer than average poly(A) tails, which is believed to contribute to their stability (David et al 2006;Beilharz and Preiss 2007).…”
Section: Introductionmentioning
confidence: 99%
“…We performed the analysis using MArray, a software that allows the user to analyze single or paired microarray data sets (Wang et al, 2002). MArray defines the quality of microarray experiments and assesses the reproducibility of replicate experiments.…”
Section: Dna Microarray Experiments and Analysismentioning
confidence: 99%
“…For hybridization, the microarrays were incubated in 50 l of hybridization solution (1% sonicated salmon sperm, 24.75% formamide, 4.95ϫ SSC, 0.099% SDS, and 0.99 mM dithiothreitol) for 10 -18 h at 42°C. After washing (1 min in 2ϫ SSC, 0.1% SDS at 42°C; 5 min in a new solution of 2ϫ SSC, 0.1% SDS at 42°C; 10 min in 0.1ϫ SSC, 0.1% SDS; 15 s, 2 min, 2 min, and 1 min in 0.1ϫ SSC; 15 s in 0.01ϫ SSC), separate images were acquired for each dye, and fluorescence intensity ratios were obtained for all genes (Genepix-Pro3.0 Axon scanner 4000A).We performed the analysis using MArray, a software that allows the user to analyze single or paired microarray data sets (Wang et al, 2002). MArray defines the quality of microarray experiments and assesses the reproducibility of replicate experiments.…”
mentioning
confidence: 99%