SIMs Scholarly Articles

Permanent URI for this collection

http://hdl.handle.net/11071/3897

Browse

Browsing SIMs Scholarly Articles by Author "Chaba, Linda"

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    Evaluation of methods for gene selection in melanoma cell lines
    (Life science Global, 2016) Chaba, Linda
    A major objective in microarray experiments is to identify a panel of genes that are associated with a disease outcome or trait. Many statistical methods have been proposed for gene selection within the last fifteen years. While the comparison of some of these methods has been done, most of them concentrated on finding gene signatures based on two groups. This study evaluates four gene selection methods when the outcome of interested is continuous in nature. We provide a comparative review of four methods: the Statistical Analysis of Microarrays (SAM), the Linear Models for Microarray Analysis (LIMMA), the Lassoed Principal Components (LPC), and the Quantitative Trait Analysis (QTA). Comparison is based on the power to identify differentially expressed genes, the predictive ability of the genelists for a continuous outcome (G2 checkpoint function), and the prognostic properties of the genelists for distant metastasis-free survival. A simulated dataset and a publicly available melanoma cell lines dataset are used for simulations and validation, respectively. A primary melanoma dataset is used for assessment of prognosis. No common genes were found among the genelists from the four methods. While the SAM was generally the best in terms of power, the QTA genelist performed the best in the prediction of the G2 checkpoint function. Identification of genelists depends on the choice of the gene selection method. The QTA method would be preferred over the other approaches in predicting a quantitative outcome in melanoma research. We recommend the development of more robust statistical methods for differential gene expression analysis.
  • Thumbnail Image
    Item
    Field evaluation of BD FACSPrest for haemoglobin and CD4 measurement
    (Scientific and Academic Publishing Co., 2017) Chaba, Linda; Kingwara, Leonard; Muriungi, Henry
    Background:Measurements of CD4 and haemoglobin are used to determine the immunological state and information about disease progression for HIV-infected patients. Use of BD FACS Presto™ point of care (POC) device for CD4 and haemoglobin (Hb) determination can significantly improve access, uptake and coverage of laboratory services and hence management of HIV-infected patients in resource-limited settings. This study evaluated the relative bias in CD4 and Hb measurements using BD FACSPresto™ system compared to BD FACSCalibur™ CD4 analyser and Mindray BC-5380 haematology analyser respectively based on venous and capillary blood samples in a clinical hospital setting. Methods:Venous and capillary blood samples were used to determine CD4 counts and Hb levels among HIV-1 infected patients. The samples were analysed on the BD FACSPresto™ and results compared against BD FACSCalibur™ and Mindray BC-5380 for CD4 and haematology analyser respectively. Results: Results for absolute CD4 counts in both venous and capillary blood showed a high correlation (R2 = 0.922, P< 0.001) when they were analysed on BD FACSPresto™ and BD FACSCalibur™ machines. Overall, the mean difference in absolute CD4 count was 77.16 cells/mL (95%CI: 49.89, 104.42, p<0.01) when analysed on two platforms. The BD FACSCalibur™ gave a higher mean of absolute CD4 count (834.38 cells/ml) compared to BD FACSPresto™ (757.23 cells/ml) when venous sample type is used. There was a significant mean difference of Hb levels at 0.31 (P <0.001) between the two sample types when analysed on BD FACSPresto™ and Mindray BC-5380 haematology analyser. In addition, there was a high correlation (R2 = 0.920, P< 0.001) of Hb level measurements between the BD FACSPresto™ and Mindray BC-5380 haematology analyser.Conclusion: The BD FACSPresto performed satisfactorily in comparison to the conventional reference standard technologies. Venous and capillary blood sample types showed a high correlation when analysed for absolute CD4 count and Hb using BD FACSPresto™, BD FACSCalibur™ and Mindray BC-5380 haematology analyser. BD FACSPresto capillary platform can be used interchangeably with BD FACSCalibur™ venous platform for CD4 and Mindray BC-5380 for Hb measurement in resource limited settings to increase access and uptake of laboratory services.
  • Thumbnail Image
    Item
    Using copulas to select prognostic genes in melanoma patients
    (Life science Global, 2017) Chaba, Linda; Odhiambo, John; Omolo, Bernard
    Melanoma of the skin is the fifth and seventh most commonly diagnosed carcinoma in men and women, respectively, in the USA. So far, gene signatures prognostic for overall and distant metastasis-free survival, for example, have been promising in the identification of therapeutic targets for primary and metastatic melanoma. But most of these gene signatures have been selected using statistics that depend entirely on the parametric distributions of the data (e.g. t-statistics). In this study, we assessed the impact of relaxing the parametric assumptions on the power of the models used for gene selection. We developed a semi-parametric model for feature selection that does not depend on the distributions of the covariates. This copula-based model only assumed that the marginal distributions of the covariates are continuous. Simulations indicated that the copula-based model had reasonable power at various levels of the false discovery rate (FDR). These results were validated in a publicly-available melanoma dataset. Relaxing parametric assumptions on microarray data may yield procedures that have good power for differential gene expression analysis.