Questions tagged [microarray]

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

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13
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2answers
20k 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 ...
77
votes
3answers
58k views

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 ...
16
votes
1answer
12k views

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 "...
1
vote
1answer
541 views

How can I use synthetic data to validate my classification model?

Through R and based on a microarray gene expression dataset (60 samples in total-30 cancer and 30 control samples) and R package caret, i have performed a feature selection regarding a binary ...
5
votes
2answers
250 views

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 ...