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Questions related from Veera Manikandan R
I need to do epistasis analysis between two sets of SNPs (each contains ~1000 SNPs). I am interested in pairwise interactions between the SNPs on different sets and not between SNPs on same set. I...
09 September 2015 2,739 2 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...
04 April 2015 1,491 11 View
Is there a way to find out if a SNP is located in an miRNA coding region? For example, if I have a list of SNPs, is it possible to find out how many of my SNPs are located in an miRNA coding...
12 December 2014 7,548 8 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...
12 December 2014 8,646 6 View
Recently I was trying to visualize the GWAS significant SNPs on chromosome to get a global view and to look for any clustering of significant SNPs in any region of chromosome. I found a software...
12 December 2014 4,757 6 View
In genetic association studies we explain the association of a polymorphic allele or genotype in terms of odds ratio i.e., the odds of getting a disease when compared with a reference allele or...
12 December 2014 8,590 4 View
Here the outcome variable is continuous and bi-modally distributed with clustering at the both extreme ends of histogram. The predictor is a categorical variable which has three categories such as...
11 November 2014 3,862 5 View
I know that the bed file (Binary ped) of plink is different from UCSC's bed file. I would like to create a bed file of genomic co-ordinates of all the SNPs in plink data. Can any one help me with...
07 July 2014 1,562 8 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...
06 June 2014 4,827 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...
06 June 2014 9,194 8 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...
05 May 2014 4,612 6 View
I have a basic doubt regarding reporting of odds ratio. We see that odds ratio can be expressed both in terms of risk (>1) or protection (1) to other (
05 May 2014 8,388 2 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...
05 May 2014 9,308 6 View
Two groups ( controls and test) of animals were treated with a particular drug (dose=x g/kg body weight) over a time period of 5 weeks. The blood level of drug is measured at time points 1, 2, 3,...
01 January 2014 9,593 5 View
I have a data of 100 yes/no type answers collected from 100 students, which forms a matrix of 100X100. I have around 200 missing data, and the missing data cannot be ignored since it very badly...
01 January 2014 7,581 4 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...
11 November 2013 5,186 1 View
Can anyone explain me what is the difference between additive(or Co-dominant) and log-additive(or multiplicative) models in genetic association analysis.
06 June 2013 7,288 3 View
Suppose I'm interested in a particular region of human genome, and I want know about the known polymorphisms in the region from GWAS data, how can I do that?
04 April 2013 1,617 1 View
What is meant by the term asymtotic test in bio-statistics?
04 April 2013 3,409 5 View
The Cochran Armitage Trend Test is used in genetic association studies where you expect a trend between the groups viz. wild, hetero and homozygous. But if any of the counts in the 2x3 table are...
04 April 2013 4,732 7 View
In the ternary plot diagram that is computed by R, how can i label the individual marker or dots in the plot, for example to label with the name of snp or rs number of snp?
04 April 2013 4,495 3 View
Is it correct to calculate the sample size for the mean difference by using precision? How is the precision value described (in terms of percentage)?
01 January 2013 410 4 View
Are all cell lines suitable for transfection to establish a stable expression? I wanted to stably express a gene in a human neuroblastoma cell line. Any suggestions?
01 January 2013 7,819 6 View
It is said that, unless specified, restriction enzymes should be stored in -20 and storing in -80 will spoil the enzymes. Why is that so?
01 January 2013 6,228 2 View
After positive selection in a few passages, we get a clone stably expressing the gene of interest. But what does that actually mean? Does that mean that the plasmid is integrated into the genome...
01 January 2013 3,996 6 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?
01 January 2013 8,955 88 View
