Journal: BMC Bioinformatics

Article Title: Assessing affymetrix GeneChip microarray quality

doi: 10.1186/1471-2105-12-137

Figure Lengend Snippet: Distribution of GNUSE values . Histograms of GNUSE values from (A) 11299 HGU133a arrays from 338 studies and (B) 11029 HGU133plus2 arrays from 471 studies. Most GNUSE values are of acceptable quality (close to one), but the long right tail suggests some very poor quality probesets.

Article Snippet: To assess the overall quality of publicly available microarray data, we computed GNUSE values for all Affymetrix HGU133a and HGU133plus2 MIAME-compliant arrays available from the Gene Expression Omnibus (GEO) [ ] in December, 2009.

Techniques:

Journal: BMC Bioinformatics

Article Title: Assessing affymetrix GeneChip microarray quality

doi: 10.1186/1471-2105-12-137

Figure Lengend Snippet: Distribution of median GNUSE values . Histograms of median GNUSE values from (A) 11299 HGU133a arrays or (B) 11029 HGU133plus2 arrays. The red vertical line represents the threshold of 1.25 - arrays with a median GNUSE greater than this threshold are considered poor quality. In both cases, this threshold appears to separate the majority of good quality arrays from the long right tail of poor quality arrays.

Article Snippet: To assess the overall quality of publicly available microarray data, we computed GNUSE values for all Affymetrix HGU133a and HGU133plus2 MIAME-compliant arrays available from the Gene Expression Omnibus (GEO) [ ] in December, 2009.

Techniques:

Journal: Oncotarget

Article Title: Long non-coding RNA expression profiles of hepatitis C virus-related dysplasia and hepatocellular carcinoma

doi:

Figure Lengend Snippet: Expression values of LINC01419 (A), AK021443 (B), and AF070632 (C) in the five stages of HCC based on microarray data from73 patient samples (10 healthy liver samples, 12 cirrhotic liver samples, 17 dysplastic liver samples, 16 early HCC samples, and 17 advanced HCC samples). For A, B, and C. the p -values were calculated using the Mann-Whitney test. D. LINC01419 expression in 55 pairs of HBV-related HCC and 15 pairs of HCV-related HCC. The expression level of LINC01419 was analyzed by qRT-PCR. The p -values were calculated using the Wilcoxon signed-rank test. E. Genomic context of LINC01419. A CpG methylation site was found upstream of the LINC01419 coding sequence.

Article Snippet: For these Affymetrix microarray platforms (HGU133plus2.0), we re-annotated the entire collection of probes using the ncFANs utility.

Techniques: Expressing, Microarray, MANN-WHITNEY, Quantitative RT-PCR, CpG Methylation Assay, Sequencing