Fetching Illumina probe ID information

Check which annotation package you need for your microarray data at http://www.bioconductor.org/packages/release/data/annotation/ The results I'm looking at are from a Illumina HumanHT12v3 BeadChip microarray (illuminaHumanv3.db). Make sure you're running the latest version of R (R version 2.13.0 (2011-04-13)) and Bioconductor (Bioconductor version 2.8). Sourced from Bioconductor mailing list thread -> [BioC] [Fwd: help in annotation...

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Check whether two genes belong to the same pathway

Updated: 2013 December 16th to include the Reactome database Source: Bioconductor mailing list: thread [BioC] How to quikly know whether two genes are in the same pathway or not? Using reactome If you ran the above code, you should get this warning: KEGG.db contains mappings based on older data because the original resource was removed...

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Visualising FANTOM3 human CAGE data

First download the relevant tables from here. Download tss_library_expr_summary.tsv.bz2, tss_summary.tsv.bz2 and rna_lib_summary.tsv.bz2 and bunzip2 the files. According to information derived from rna_lib_summary.tsv there are 13,897 CAGE tags from the prostate gland (rna_lib_id = HBA). Double check this: Genomic coordinates of TSSs can be obtained from tss_summary.tsv. Here's a script which generates bedgraph files of all...

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The Normal Distribution

Updated 2014 December 19th The normal or Gaussian distribution is commonly occurring continuous probability distribution. The skewness, which is a measure of symmetry (or there lackof), of a normal distribution is zero since the distribution is symmetrical, i.e. it looks the same to the left and right of the centre. Kurtosis can be used to...

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