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Microarray data analysis (median detection pvalue)

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.

gene
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updated by Ram Ram • written by payman.nickchi • payman.nickchi

2 answers

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.

• 0 views • link
updated by Ram Ram • written by Manvendra Singh Manvendra Singh

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.

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updated by Ram Ram • written by payman.nickchi • payman.nickchi

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
• 0 views • link
updated by Ram Ram • written by Manvendra Singh Manvendra Singh

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