How to do gene expression analysis in microarray?
Microarray data analysis • begin with a data matrix (gene expression values versus samples) Typically, there are many genes (>> 20,000) and few samples (~ 10) Microarray data analysis • begin with a data matrix (gene expression values versus samples) Preprocessing Inferential statistics Descriptive statistics Microarray data analysis: preprocessing
How are microarray data used in Biological Studies?
Such procedure can be circular in logic; better procedure is to identify differences between groups defined on biological grounds. Microarray data is often used as a guide to further, more precise studies of gene expression by qt-PCR or other methods.
Why are permutation tests used in microarray studies?
Permutation testing is an approach that is widely applicable and copes with distributions that are far from Normal; this approach is particularly useful for microarray studies because it can be easily adapted to estimate significance levels for many genes in parallel.
Is the log transform too strong in microarray plots?
However the gene abundances on the log scale usually show greater variation near the bottom end, giving rise to the characteristic ‘funnel’ shape of many microarray plots. The log transform is too ‘strong’, and partly reverses the inequality of measurement variances.
How to global normalize a microarray data set?
Data analysis: global normalization Global normalization procedure Step 1: subtract background intensity values (use a blank region of the array) Step 2: globally normalize so that the average ratio = 1 (apply this to 1-channel or 2-channel data sets) Scatter plots
What are the advantages of using a microarray?
Advantages of microarray experiments Easy Submit RNA samples to a core facility Cheap! Chip representing 20,000 genes for $300
How are oligonucleotides deposited in a microarray array?
The array consists of cDNA or oligonucleotides Oligonucleotides can be deposited by photolithography The sample is converted to cRNA or cDNA (Note that the terms “probe” and “target” may refer to the element immobilized on the surface of the microarray, or to the labeled biological sample; for clarity, it may be simplest to avoid both terms.)
Where can I find data on gene expression?
• Find UniGene at NCBI: www.ncbi.nlm.nih.gov/UniGene • UniGene clusters contain many ESTs • UniGene data come from many cDNA libraries. Thus, when you look up a gene in UniGene you get information on its abundance and its regional distribution. Microarrays: tools for gene expression