15 Questions 21 Answers 0 Followers
Questions related from Veera Manikandan R
In gene-gene interaction (epistasis) analysis we commonly use the co-dominant models for both the SNPs that are tested for interaction. For example in R, we can do by constructing GLM...
31 July 2015 2,703 3 View
Bar graphs don't inform adequately. They just represent the mean and the standard error. We need to know even more from the graphs. In fact, the bar graphs starts from 0 at the bottom, which...
26 April 2015 7,785 9 View
I have a very basic question. In genomic analysis we deal with coordinates. But I am little confused with the understanding about coordinates numbering system between positive and negative strand....
19 December 2014 2,165 1 View
Suppose if I want to screen variants that are present upstream in promoter region of a set of genes, till what extent I can search for variants upstream of each gene. Can the threshold be a common...
09 December 2014 1,951 6 View
I have GWAS data from Ilumina platform (The HumanOmni2.5-8 (Omni2.5) BeadChip). The data is in Plink format. When i tried imputation with IMPUTE2 i got a concordance rate of around 50 percent,...
16 August 2014 5,136 2 View
Can anyone suggest a method to calculate a sample size to study an effect of epistasis between two polymorphisms over a clinical phenotype (ex: drug response). Suggestion of any reference will be...
03 June 2014 1,941 2 View
Lets say I am analyzing a genetic polymorphism data where I have genotyped 120 cases and 50 controls. I guess it is not statistically right to compare a larger number of cases to fewer controls as...
01 June 2014 6,067 7 View
Validating logistic regression models. I derived a logistic regression model for predicting clinical response to a drug. I have two groups: responders and non-responders, classified according to a...
29 May 2014 1,630 6 View
I am studying association of two polymorphisms with 6 adverse effects of a drug. In this case, if want to adjust for multiple testing by Bonferroni's method, should I multiply p value by 2 (since...
24 May 2014 4,508 1 View
We are aware that most of the genetic association studies are under-powered just because of the fact the sample size is inadequate. The major reason for the power to be small is because, in most...
03 May 2014 9,993 6 View
Study design: case-control / cross-sectional / genetic association Locus: bi-allelic phenotype: an adverse effect of a drug high risk allele frequency: 0.65 (this is not the wild allele, but...
30 April 2014 9,376 2 View
In genetic analysis, the allelic odds ratio is calculated from a 2X2 table where the counts of the cells are derived from genotype counts. Just wondering in that case how to adjust for the effects...
08 November 2013 3,587 1 View
I have two SNPs - one on Chr-11 and another on Chr-15 - for which I have to see the epistatic effect on a phenotype. I know it makes no sense to see the epistasis for two SNPs that are close...
21 October 2013 4,081 2 View
Is there a standard formula to calculate the percentage of agarose gel to be cast ?
03 January 2013 7,592 11 View
Many alternatives are available commercially, including non-tox, fast-blast, EZ-vision, Redsafe-DNA, etc. but I am not sure which is best. Does anyone have any experience with this? Any suggestions?
02 January 2013 6,994 87 View
