Microarray data analysis (median detection pvalue)

Question

[payman.nickchi]

Hi. I am currently doing Microarray data analysis on some dataset in GEO and I came up in one paper with the method "median detection p-values" for reducing the number of genes. As it says this procedure is useful for finding absent probes!. Here is the link to paper: http://www.ncbi.nlm.nih.gov/pubmed/22005334

I do not know how does it work and what is the notion of it. It would be grateful if anyone can propose a reference to read more about it. After a complete search I could not find any reliable result about it.

Answer 1

[Manvendra Singh]

It's better to take raw files from GEO datasets and analyze by yourself, It takes 20-30 mins to process the files in R bioconductor

Here is how to analyze them. One very nice Tutorial is from Obi Griffith, which is here.

Answer 2

[payman.nickchi]

Unfortunately the CELL files are not available for this study, only txt raw data is available. I am familiar with bioconductor project and my question is not how to analyse microarray data with bioconductor project. I am searching for median detection method.

[Manvendra Singh]

okay

• grab the raw files
• transform their value on log2 scale
• install limma package
• do the median centric normalization
• you can use normalizeQuantiles , it makes upper quantile adjusted to median value
• make a boxplot if data is normalized (medians of boxes should fall in single line)
• then you can go for differentially expressed genes or relative enrichments