Statistical Analysis Stack Exchange
Statistical Analysis Stack Exchange

Questions tagged [microarray]

DNA microarrays are used to measure the expression levels of large numbers of genes simultaneously.

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Best way to present a random forest in a publication?

I am using the random forest algorithm as a robust classifier of two groups in a microarray study with 1000s of features. What is the best way to present the random forest so that there is enough information to make it reproducible in a paper? Is…
danielsbrewer
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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 values of genes in the experimental sample over…
stlandroidfan
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How does quantile normalization work?

In gene expression studies using microarrays, intensity data has to be normalized so that intensities can be compared between individuals, between genes. Conceptually, and algorithmically, how does "quantile normalization" work, and how would you…
Stephen Turner
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Clustering genes in a time course experiment

I have seen a few queries on clustering in time series and specifically on clustering, but I don't think they answer my question. Background: I want to cluster genes in a time course experiment in yeast. There are four time points say: t1 t2 t3 …
suncoolsu
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Is the overlap between two gene expression samples significant?

I have performed an experiment to study the response of a yeast (that contains 5000 genes) to stress caused by heat shock. I have one list of 48 genes that are overexpressed at 37ºC and another list of 145 genes that are overexpressed at 42ºC. There…
Laura
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Test for significant excess of significant p-values across multiple comparisons

I have what feels like a simple question, but was unable to find answers easily. The situation Let's say I have a gene microarray dataset with tens of thousands of genes and small (<100) number of samples. I am interested in simple mean differences…
Karolis Koncevičius
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Adding high-dimensional data to mutivariate Cox model

I have a survival cancer clinical trials dataset from which I have generated Cox models using forward likelihood ratio testing within R. These models are based on 'traditional' cancer variables (eg. age, histology, metastasis etc). I would like to…
EdS
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Should false discovery be controlled at the data acquisition level, or should this be at the data interpretation level?

Should false discovery be controlled at the data acquisition level, or should this be at the data interpretation level? I have an experiment in which microarrays were used to quantify the expression of about 30,000 genes (variables) in two groups of…
user4045
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Is cross-validation an effective approach for feature/model selection for microarray data?

I've been working with WEKA to build class predictors using this (rather old..) breast cancer dataset. The dataset is divided into a training and a test set. I've been testing different learning schemes (mostly focused on feature selection) using…
Ben
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Comparing numbers of p-values from many linear models

My current dataset has three conditions, and we've measured the activity levels of 10,000 genes in each condition. Replicated 8 times. Using 10,000 linear models, we determine for each pair of conditions (ie for each of three contrasts) the number…
Yannick Wurm
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Testing for equality of variance in permutations (microarray analysis with bioconductor)

I have measured whole-genome gene expression in two groups of animals, n=6 in each group. My goal is to detect differentially expressed genes - pretty standard analysis. The typical thing to do, and what I suspect is a situation where 'everybody…
yotiao
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How to highlight predefined groups in PCA individual map?

This has a simple answer but it has been eluding me nonetheless. I have been trying to build a PCA plot from scratch with the ability to plot predefined groups in different colors. I can plot PCA but I want it to plot with predefined groups…
Shafi
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shorth function in R and microarray analysis

I'm trying to reproduce an analysis (a transcriptomic analysis) that I found in a research paper. The methods section says: After normalization an expression threshold for each cell line was calculated to get rid of low intensity probes that can…
Juan Fernandez Tajes
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Correlation analysis on two different groups of continuous heterogeneous variables with different range/scales in R

I would like to perform in R a initial simple correlation analysis, between a gene signature that i have identified, and some continuous clinical parameters, measured on the same patients, to identify any interesting correlation patters. However, my…
Jason
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Methods for tri-clustering a 3 dimensional array

I have a 5000 X 32 X 10 3D array of gene expression data that I would like to apply clustering and dimensionality reduction on. The dimensions represent the following: I have 5000 genes, measured in 32 different mutant strains, each in one of 10…
kmace
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