microarray suite version 5 mas5 algorithms  (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: BMC Bioinformatics

Article Title: Effects of filtering by Present call on analysis of microarray experiments

doi: 10.1186/1471-2105-7-49

Figure Lengend Snippet: Distribution of MAS5 log 2 (signals) before and after filtering . A) No filter. B) Filtering with threshold of ≥ 50% Present in at least one treatment group. C) Filtering by average signal with threshold at ≥475 in at least one treatment group. The number of probe-sets at each value of Log2(signal) are plotted. Black = Present, gray = Marginal, white = Absent.

Article Snippet: The Affymetrix Microarray Suite version 5 (MAS5) algorithm uses the probe-pair data in different ways to calculate the detection call and the signal.

Techniques:

Journal: BMC Bioinformatics

Article Title: Effects of filtering by Present call on analysis of microarray experiments

doi: 10.1186/1471-2105-7-49

Figure Lengend Snippet: Percent of probe sets remaining after filtering . Percent of probe sets remaining after filtering using selected thresholds for A) Fraction Present. B) MAS5 Signal. C) RMA value.

Article Snippet: The Affymetrix Microarray Suite version 5 (MAS5) algorithm uses the probe-pair data in different ways to calculate the detection call and the signal.

Techniques:

Journal: BMC Bioinformatics

Article Title: Effects of filtering by Present call on analysis of microarray experiments

doi: 10.1186/1471-2105-7-49

Figure Lengend Snippet: Probe sets remaining at different filtering thresholds a .

Article Snippet: The Affymetrix Microarray Suite version 5 (MAS5) algorithm uses the probe-pair data in different ways to calculate the detection call and the signal.

Techniques:

Journal: BMC Bioinformatics

Article Title: Effects of filtering by Present call on analysis of microarray experiments

doi: 10.1186/1471-2105-7-49

Figure Lengend Snippet: Highly significant (p ≤ 0.001) probe sets lost at different filtering thresholds a .

Article Snippet: The Affymetrix Microarray Suite version 5 (MAS5) algorithm uses the probe-pair data in different ways to calculate the detection call and the signal.

Techniques:

Journal: BMC Bioinformatics

Article Title: Effects of filtering by Present call on analysis of microarray experiments

doi: 10.1186/1471-2105-7-49

Figure Lengend Snippet: Number of significant probe sets after filtering . A) Filtering by fraction Present vs. by average MAS5 signal. The probe sets called significantly different (at the p-values shown) between the interferon treated and untreated samples in the 10 sample experiment are plotted against the threshold of Fraction Present (FP) or average signal (S), followed by threshold value. The horizontal line at 1230 indicates the number of probe sets at p ≤ 0.001 in the unfiltered data. Paired thresholds remove comparable numbers of probe sets, e.g. FP>0 and S254. B) Filtering by fraction Present vs . by average RMA value. (FP) Fraction Present, (R) average RMA value, followed by threshold value. The line at 1641 indicates the number of probe sets at p ≤ 0.001 in the unfiltered data.

Article Snippet: The Affymetrix Microarray Suite version 5 (MAS5) algorithm uses the probe-pair data in different ways to calculate the detection call and the signal.

Techniques:

Journal: BMC Bioinformatics

Article Title: Effects of filtering by Present call on analysis of microarray experiments

doi: 10.1186/1471-2105-7-49

Figure Lengend Snippet: Effect of Filtering on false discovery rate (FDR) . Filter method and values (x-axis): Fraction Present (FP), signal (S) or RMA value (R) followed by threshold value; separate lines are shown for each. Closed circles represent values from fraction Present filtering, open diamonds from average signal or average RMA. P-values: 0.05 (blue), 0.01 (pink), and 0.001 (green). A) IFN data, MAS5, B) IFN data, RMA, C) Smoking data, MAS5. Note that the smoking data was scaled to 100 instead of 1000 used for the other data sets.

Article Snippet: The Affymetrix Microarray Suite version 5 (MAS5) algorithm uses the probe-pair data in different ways to calculate the detection call and the signal.

Techniques: