Biomedical subjects

Harris A Jaffee

Publications and source records attributed to Harris A Jaffee.

3 recordsLinked to original sources

PubMed2006

Comparison of Affymetrix GeneChip expression measures.

MOTIVATION: In the Affymetrix GeneChip system, preprocessing occurs before one obtains expression level measurements. Because the number of competing preprocessing methods was large and growing we developed a benchmark to help users identify the best method for their application. A webtool was made available for developers to benchmark their procedures. At the time of writing over 50 methods had been submitted. RESULTS: We benchmarked 31 probe set algorithms using a U95A dataset of spike in controls. Using this dataset, we found that background correction, one of the main steps in preprocessing, has the largest effect on performance. In particular, background correction appears to improve accuracy but, in general, worsen precision. The benchmark results put this balance in perspective. Furthermore, we have improved some of the original benchmark metrics to provide more detailed information regarding precision and accuracy. A handful of methods stand out as providing the best balance using spike-in data with the older U95A array, although different experiments on more current arrays may benchmark differently. AVAILABILITY: The affycomp package, now version 1.5.2, continues to be available as part of the Bioconductor project (http://www.bioconductor.org). The webtool continues to be available at http://affycomp.biostat.jhsph.edu CONTACT: rafa@jhu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗

PubMed2004

A benchmark for Affymetrix GeneChip expression measures.

MOTIVATION: The defining feature of oligonucleotide expression arrays is the use of several probes to assay each targeted transcript. This is a bonanza for the statistical geneticist, who can create probeset summaries with specific characteristics. There are now several methods available for summarizing probe level data from the popular Affymetrix GeneChips, but it is difficult to identify the best method for a given inquiry. RESULTS: We have developed a graphical tool to evaluate summaries of Affymetrix probe level data. Plots and summary statistics offer a picture of how an expression measure performs in several important areas. This picture facilitates the comparison of competing expression measures and the selection of methods suitable for a specific investigation. The key is a benchmark data set consisting of a dilution study and a spike-in study. Because the truth is known for these data, we can identify statistical features of the data for which the expected outcome is known in advance. Those features highlighted in our suite of graphs are justified by questions of biological interest and motivated by the presence of appropriate data.

Algorithms↗

PubMed2004

Patients' perceptions of the value of current vision: assessment of preference values among patients with subfoveal choroidal neovascularization--The Submacular Surgery Trials Vision Preference Value Scale: SST Report No. 6.

OBJECTIVE: To improve understanding and awareness of the impact of subfoveal choroidal neovascularization (CNV) on health-related quality of life, we sought to measure the preference value that patients with subfoveal CNV assigned to their health and vision status. PATIENTS AND METHODS: Patients with subfoveal CNV completed telephone interviews about their quality of life prior to enrollment and random treatment assignment in the Submacular Surgery Trials, a set of multicenter randomized controlled trials evaluating outcomes of submacular surgery compared with observation. The interviewers asked patients to rate their current vision on a scale from 0 (completely blind) to 100 (perfect vision). The interviewers also asked them to rate complete blindness and then perfect vision, assuming their health otherwise was the same as it was at the time of the interview, on a scale from 0 (dead) to 100 (perfect health with perfect vision). Scores were converted to a 0 to 1 preference value scale for health and vision status, where 0 represents death and 1 represents perfect health and vision. RESULTS: Of 1015 participants enrolled in the Submacular Surgery Trials, 996 completed interviews that included the rating questions, and 792 (80%) answered all 3 rating questions in a manner permitting calculation of a single overall preference value for their current health and vision status on a scale from 0 (dead) to 1 (perfect). The mean preference value was 0.64 (median, 0.68; interquartile range, 0.51-0.80). The preference values correlated with age (Pearson correlation coefficient, -0.11; P = .002), patients' self-rated perception of overall health (Spearman correlation coefficient, 0.36; P<.001), and self-reported perception of vision (Spearman correlation coefficient, 0.47; P<.001). The preference values were significantly lower with poorer visual acuity in the better eye and greater evidence of dysfunction on either the Hospital Anxiety and Depression Scale or the Physical or Mental Component Summary scales of the Short Form-36 Health Survey but did not differ significantly by gender or other baseline characteristics such as race, treatment assignment, or size of the CNV lesion. CONCLUSIONS: Vision loss from subfoveal CNV is associated with patient preference values that are as low as or lower than values previously reported for other serious medical conditions such as dialysis-dependent renal failure and AIDS, indicating that both unilateral and bilateral CNV have a profound impact on how patients feel about their overall health-related quality of life.

Adult↗