microarray suite software version 5 0  (Thermo Fisher)

Journal: BMC Genomics

Article Title: Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues

doi: 10.1186/1471-2164-10-324

Figure Lengend Snippet: Overlay of expression detection between MPSS and microarray for sense and antisense transcripts malignant and normal breast epithelium . Human transcriptome clusters (HTR) were used to measure the concordance in detecting sense and antisense transcripts for the Breast Cancer DSA (green), Affymetrix HG U133 Plus 2.0 (blue) and MPSS (red) in both the malignant breast epithelium and normal luminal epithelium. The presence of a MPPS tag was determined if a MPSS tag had at least a count of 3 tpm in these samples. For the two microarray platforms, a HTR cluster was called present when its containing sense (top section) or antisense (bottom section) probe set obtained a present calls with the MAS5 algorithm.

Article Snippet: Secondly, analysis was performed on the Breast Cancer DSA with the Affymetrix Microarray Suite version 5 (MAS5) algorithms, which uses the probe-pair data to calculate the detection call.

Techniques: Expressing, Microarray

Journal: Arthritis Research & Therapy

Article Title: Exogenous glucosamine globally protects chondrocytes from the arthritogenic effects of IL-1β

doi: 10.1186/ar2082

Figure Lengend Snippet: Changes in global expression patterns of chondrocytes induced by glucosamine and IL-1β. A two-way agglomerative hierarchical clustering of samples. The treatment groups are indicated by the legend on the left (also see text; Gln, glucosamine). Only the normalized signal values of genes with a significant ( P < 0.0001) treatment effect were included. Each row represents a sample and each column a gene. Color intensities reflect relative signal values, whereby red represents a higher level of gene expression, and green a lower level relative to the mean across all samples for each gene. On the right, hierarchical clustering of the samples is indicated both within and among treatment groups. Longer lines represent greater dissimilarity between samples. For these samples, one of the untreated control samples and two samples from the glucosamine-alone groups were eliminated from the final analysis because they did not satisfy the quality control criteria of the microarray analysis.

Article Snippet: Microarray Suite (version 5; Affymetrix) was used to generate *.cel files, and a computer program (Probe Profiler, version 1.3.11; Corimbia, Inc Berkeley, CA, USA) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.

Techniques: Expressing, Microarray