Endogenous orienting modulates the Simon effect: critical factors in experimental design.
Ontology highlight
ABSTRACT:
SUBMITTER: Abrahamse EL
PROVIDER: S-EPMC2668658 | biostudies-other | 2008 May
REPOSITORIES: biostudies-other
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Project description:BackgroundThe analysis of large-scale gene expression data is a fundamental approach to functional genomics and the identification of potential drug targets. Results derived from such studies cannot be trusted unless they are adequately designed and reported. The purpose of this study is to assess current practices on the reporting of experimental design and statistical analyses in gene expression-based studies.MethodsWe reviewed hundreds of MEDLINE-indexed papers involving gene expression data analysis, which were published between 2003 and 2005. These papers were examined on the basis of their reporting of several factors, such as sample size, statistical power and software availability.ResultsAmong the examined papers, we concentrated on 293 papers consisting of applications and new methodologies. These papers did not report approaches to sample size and statistical power estimation. Explicit statements on data transformation and descriptions of the normalisation techniques applied prior to data analyses (e.g. classification) were not reported in 57 (37.5%) and 104 (68.4%) of the methodology papers respectively. With regard to papers presenting biomedical-relevant applications, 41(29.1 %) of these papers did not report on data normalisation and 83 (58.9%) did not describe the normalisation technique applied. Clustering-based analysis, the t-test and ANOVA represent the most widely applied techniques in microarray data analysis. But remarkably, only 5 (3.5%) of the application papers included statements or references to assumption about variance homogeneity for the application of the t-test and ANOVA. There is still a need to promote the reporting of software packages applied or their availability.ConclusionRecently-published gene expression data analysis studies may lack key information required for properly assessing their design quality and potential impact. There is a need for more rigorous reporting of important experimental factors such as statistical power and sample size, as well as the correct description and justification of statistical methods applied. This paper highlights the importance of defining a minimum set of information required for reporting on statistical design and analysis of expression data. By improving practices of statistical analysis reporting, the scientific community can facilitate quality assurance and peer-review processes, as well as the reproducibility of results.
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Project description:An increase in early-onset colorectal cancers (eoCRC), defined as a CRC before 50 years, is confirmed globally.
CRC pathogenesis has been associated with several risk factors (family history, germline pathogenic variants, obesity, alcohol, physical activity, red meat, and a Western diet).
Design: an international, multicenter, retrospective case-control study of prospectively enrolled patients; low-risk intervention study as it will perform a fecal occult blood test Endpoint: predictive power of a semi-quantitative food frequency questionnaire (SQFFQ) developed for eoCRC.
Cases: Patients with a recent diagnosis of eoCRC (within 2 years from enrollment).
Controls: matched by age (matching range ± 5 years) and sex. Healthy volunteers will be mainly enrolled among workers within the participating hospital center. The enrolled healthy volunteers will perform a fecal occult blood test.
Variables of interest: age, sex, ethnicity, BMI at the time of eoCRC diagnosis and at 18 years old, country, tobacco smoking at the time of eoCRC diagnosis and at 18 years old, sitting time, TV-viewing time, moderate-to-vigorous physical activity (MVPA), waist circumference (cm), home blood pressure levels (mmHg), fasting blood glucose (mg/dl), regular consumption of aspirin/NSAID, calcium and folate supplements, oral contraceptive agents, post-menopausal hormones and years of consumptions, if the filled questionnaire reflects diet for the last 5-10 years before.
Cases only: date of eoCRC diagnosis, symptoms at diagnosis, eoCRC localization, eoCRC stage, histological diagnosis, type of surgery, and date (if performed), chemotherapy and radiotherapy (if performed), vital status and duration of follow-up, family history of CRC and other cancers (uterus, ovary, stomach, small intestine, urinary tract/bladder/kidney, bile ducts, brain, pancreas, skin tumors), type of germline pathogenetic variant (if performed).
Before the case-control study, three non-consecutive 24-hour Dietary Recalls (24hDRs) will validate the SQFFQ.
The SQFFQ will be administered to the validation study group during three non-consecutive calls, including one non-weekday (30-minute 24-h-recall computer-aided personal interview).
Primary Objective To measure the relative risk of specific dietary and lifestyle factors (smoking habit, alcohol intake, physical activity) for early-onset colorectal cancer in countries where eoCRC incidence is increasing versus stable/decreasing
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