The genetics tag has no wiki summary.
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1answer
34 views
Detecting variants of unknown significance
I have two groups of people, a healthy population which has carriers of disease and non-carriers, and I have a sick population. I know the frequency of genetic variants in both groups. I want to ...
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18 views
Balanced chromosomal translocation [closed]
I have two cute sons,9 and 1 years old, unfortunately both of them inherited balanced trans location from my wife. I'm worry about their abilities to be parent of next generation in terms of ...
1
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1answer
176 views
How to interpret false positive from QQ-plot in genome-wide association studies?
I am doing SNP association study, and the estimated p-values for each SNP are plotted as a QQ-plot. The question is, can one interpret false positive hits from a QQ-plot in GWAS (Genome-Wide ...
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0answers
32 views
Statistical inference about degree of a node in a genetic network
I am working on Gene-Gene interaction networks. I build a graph by adding edges between genes (nodes) representing statistical interaction in prediction of a quantitative parameter value (say, brain ...
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0answers
112 views
expected effect of each SNP in a GWAS
It was mentioned in a genetics class that in a genetic association analyses of a trait with all SNPs, it is possible to compute the expected effect of each SNP with the trait using the correlation ...
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0answers
12 views
Approximation of explained variance [duplicate]
I am reading a paper on "multi-SNP" GWAS data analysis method,
The author fitted a linear model $y = \beta_g g + \epsilon$, where $g$ is a genotype vector for a single gene, $\beta_g$ is the true ...
3
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1answer
83 views
Approximation of explained variance
I am reading a paper on "multi-SNP" GWAS data analysis method,
The author fitted a linear model $y = \beta_g g + \epsilon$, where $g$ is a genotype vector for a single gene, $\beta_g$ is the true ...
1
vote
1answer
168 views
Comparing two sets of data for similarity
I have two independent sets of gene expression data (biological replicates) that were generated at the same time. Each gene is sampled dozens of times on the machine (technical replicates). Data are ...
1
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3answers
114 views
How to find genes associated with PC1 and PC2 after the PCA on microarray?
I have run a PCA on my microarray data and found the clustering pattern for my samples.
Now I need to find out the genes which are associated with first principal component and likewise till 4th PC.
...
4
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1answer
45 views
Enrichment Analysis by Gene Duplication Level
Biological Background
Over time, some plant species tend to duplicate their entire genomes, gaining an additional copy of each gene. Due to the instability of this setup, many of these genes are then ...
2
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0answers
166 views
How to get correct Covariance components in SAS Proc mixed? Struggling with infinite likelihoods and negative variance components
I am trying to estimate covariance components from PROC MIXED and having trouble with convergence problems in the REML approach when I use the NOBOUNDS option. Let me explain why I am using NOBOUNDS ...
1
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1answer
43 views
How do you determine the effect of a simple predictor variable after a PLS analysis?
So, I am running PLS on a genetic dataset with phenotypic and genotypic information. I have about 1000 binary predictors (X), representing molecular markers, for each individual. My indicator ...
0
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1answer
60 views
Multiple comparison with genotype data
I am looking at the effect of genotype on a continuous variable. In total 16 comparisons were done involving 9 different SNPs. The number of significant events was 3 out of 16 tests (Mann-Whitney ...
2
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0answers
63 views
Making sense of a factor analysis application
I'm a biochem guy so the stats in this paper are giving me a real hard time.
Kliman, RM, Irving, N, and Santiago, M. Selection Conflicts, Gene
Expression, and Codon Usage Trends in Yeast. J Mol ...
3
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2answers
977 views
Is a heat-map of gene expression more informative if Z-scores are used instead of actual expression measurement values?
I have a heat-map of gene expression measurements (log2-transformed microarray signals, after inter-microarray data normalization, etc.) that I am using to illustrate the expression of 72 genes ...
1
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1answer
176 views
How can I calculate genetic similarities between groups?
I know how to calculate genetic similarity between genotypes, but I do not know how to calculate genetic similarity between groups.
From cluster analysis, I found seven groups. Now, I need to ...
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0answers
46 views
How do you obtain values for SS.PVAL, G.PVAL and I.PVAL for the snp.plotter package in R?
SS.PVAL, G.PVAL and I.PVAL as well as the associations of the SNPs are required to produce a SNP.FILE and HAP.FILE for snp.plotter but I only have the names and locations of the SNPs. Is there any ...
2
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1answer
183 views
What is a good textbook on statistical genetics for someone without a lot of biology background?
I am looking for a good book to study from to learn
about statistical genetics. I have no background in
biology, some learning in chemistry, reading some
of Griffith's book on genetic analysis but I ...
2
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0answers
123 views
PLINK meta-analysis method
I am trying to determine exactly what method PLINK uses for meta-analysis. I can't find it in the program documentation/FAQ anywhere. Inverse variance? (given the meta command only requires effect ...
3
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0answers
148 views
AIC with Mantel's tests
Mantel's tests are commonly used to compare genetic distances (say, between a number of individuals) with true or hypothesized landscape distances between those same individuals. For example, “does ...
3
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1answer
193 views
How do I get a $p$-value from the Cochran-Armitage trend test?
So, I'm working with GWAS SNP data and want to perform several tests for association between genotype and phenotype. There are two phenotypes (case and control) and 2 or three genotypes. Most of them ...
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0answers
61 views
Unique subsequences of the human genome
I am working on a project involving genomes. I am going to divide a genome into subsequences, and then do something with those subsequences. I want to know if the subsequences that I produce are going ...
4
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2answers
283 views
Appropriateness of PCA to visualize clusters in genetic data
I've seen PCA improperly applied in genetic research quite often. I wanted to clarify : when is it appropriate to use PCA as a visualization tool in your analysis?
Some examples:
1) Rarely is the % ...
2
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1answer
119 views
Nonnegative matrix factorization on a matrix with negative values
I have a gene expression profile with negative values.
Is there any way to do an Nonnegative matrix factorization (NMF) on a matrix which has a few negative values?
(I couldn't approximate the ...
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0answers
100 views
Meta-analysis using GWAS datasets of different diseases
It is well known that in Meta-analysis of Genome-wide association studies (GWAS) we combine the results of independent studies to get a pooled effect estimates (Odd ratios or betas) in order to ...
0
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1answer
86 views
Which statistical test should I use to test for associations between phenotype and genotype?
I need to select a statistical test in order to answer the question of whether the TASR238 genotype is a good predictor of the ability to taste PTC (phenotype)
...
1
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1answer
469 views
How to find differentially expressed genes in R?
Can you tell me some procedures in R, which are able to find differentially expressed genes for a given microarray data?
Moreover,If you can give some ideas related to clustering of significant ...
1
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1answer
97 views
Change in gene expression over time for different environments when each individual can only be sampled once?
A colleague has collected data on plant root gene expression. Gene expression is expected to change over time, and be dependent upon the environment that each plant is grown in (i.e fertilizer mix). ...
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2answers
232 views
Meta-analysis in R with multiple SNPs
I'm conducting a meta-analysis on two genome wide association studies (GWAS), each consisting of 150 SNPs, for which I computed summary statistics for association.
I'm using the R package meta and the ...
2
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2answers
414 views
Mahalanobis distance when n>p
I have an n by p matrix, where n is genes and p is patients. Anyone whose worked with such data knows that n is always larger than p. Using feature selection I have gotten n down to a more reasonable ...
4
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1answer
183 views
Why isn't this a problem with heritability studies?
In many studies of heritability, researchers study identical twins raised apart and raised together, and see how much a trait correlates between the two types of twins. Sometimes they use fraternal ...
3
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1answer
305 views
Wavelet smoothing at different scales
I would like to perform wavelet smoothing at different scales in R. I got the idea from this figure (panel A) were they measure the density/intensity of a particular signal at different scales.
Here ...
3
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1answer
409 views
How to convert molecular categorical variables to dummy variables for cluster analysis?
I would like to use a clustering method, e.g. 'mclust', in R to classify each individual in my dataset to k groups. I have 7 continuous and 3 categorical variables. These and other hierarchical ...
2
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3answers
299 views
Good source of information about AMOVA
I'm looking for a good source of information about Analysis of Molecular Variance (AMOVA), a kind of statistical analysis used in population genetics. Especially how are the $\phi$-statistics ...
1
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1answer
66 views
How to compare two series of gene expression levels?
I have a data set with gene expression levels measured for three different treatments, and for each treatment we have three biological replicates. Treatments are: Control, 24h at $4$°C, and 24h at ...
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0answers
104 views
Hypergeometric distribution in a genetics problem
I have a problem that I seek to solve with the hypergeometric distribution (Fisher's). I'm looking at a binary problem, disease status $0$ or $1$. I have data consisting of many allele frequencies for ...
4
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2answers
2k views
Why would one use age-squared as a covariate in a genetic association study?
Why would one use age and age-squared as covariates in a genetic association study? I can understand the use of age if it has been identified as a significant covariate, but I am at a loss as to the ...
3
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1answer
168 views
How to devise a relationship matrix without diagonal constant when fitting mixed model in R?
I have the following small data:
...
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0answers
233 views
How to compare two power law distributions?
Disclaimer: I am a biologist, so please don't hesitate to correct me if I am making unwise assumptions.
I am looking at the distribution of a unique 6mer in a series of 2100mer (I have 415 ...
3
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1answer
340 views
Use of a negative binomial model for fitting alternative splicing event
I am working on RNA-Seq data (on alternative splicing). Let's say I am looking at a particular type of alternative splicing event - exon skipping. For each intron (or junction), I look if it is ...
1
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1answer
221 views
NAs in summary of linear model generated from significant genes for continuous response variable identified using SAM
I have a gene expression data-set with log2-transformed expression values (no NAs) for 495 genes for 59 samples for which values of a continuous response variable (r) are also known (no NAs). I want ...
3
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2answers
115 views
Statistical significance of genes associated with multiple phenotypes
I have a dataset of gene-phenotype association in this format.
I am looking at some combination of phenotypes and genes shared between combination.
I would like to use a statistical test to show ...
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0answers
31 views
A measure to identify discriminating subgraphs of a larger graph?
I have genes from four species of bacteria. I constructed an undirected graph from the sequence similarity between all the genes from these bacteria. Each node in the graph is a gene and each edge is ...
3
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0answers
244 views
Using the hypergeometric distribution for skipping events in transcriptome sequencing
My question is inspired by this post. However, its a bit more complicated than that to explain. I hope I succeed.
I work with RNA-Seq data on alternative splicing in plants. For this discussion, lets ...
4
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3answers
2k views
Calculating the probability of gene list overlap between an RNA seq and a ChIP-chip data set
Hopefully someone on these forums can help me out with this basic problem in gene expression studies.
I did deep sequencing of an experimental and a control tissue. I then obtained fold enrichment ...
2
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0answers
111 views
Countering false positives in GWAS due to linkage disequilibrium
We know that due to LD, we can get significant p-values for markers near a causal marker (or a marker closes to the causal region) in GWAS studies. I've seen attempts looking at LD to do multiple ...
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0answers
95 views
Test for differences in distribution without raw data
I've got a series of statistics computed on different populations of cells, where each population contains a different genetic deletion.
The measurements I have for each population involve GFP ...
3
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0answers
84 views
What does the gene set score tell in GSA analysis?
I carrying out a gene set analysis to investigate if a list of genes are differentially expressed before and after a medical treatment (paired analysis).
The list of genes was made (a priori) by a ...
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0answers
51 views
How to allocate sample size to gain most power on a two stage analysis?
In stage 1 we test many SNPs, in stage 2 we try to confirm these SNPs. Usually we start with less sample, but then it's hard to detect a signal. For example, if we can afford 3000 samples, how to ...
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3answers
707 views
False discovery rate from permutation testing?
I have conducted a search for genetic interactions using a simple dosage model:
Y ~ A + B + AB
where Y is the phenotype, in this case, gene expression values and A and B are vectors of genotype ...
