monocyte-derived macrophages of 13 male COPD patients
Extracted molecule
total RNA
Extraction protocol
phenol-chloroform extraction of total RNA
Label
see Affymetrix standard protocol
Label protocol
see Affymetrix standard protocol
Hybridization protocol
see Affymetrix standard protocol
Scan protocol
see Affymetrix standard protocol
Description
see Affymetrix standard protocol
Data processing
Data were normalized, and transcript-specific gene expression levels were calculated, using gcrma (Wu et al., J. Comput. Biol., 12, 882-93, 2005; Wu et al., Nat. Biotechnol. 22, 656-8,, 2004) or rma (Bolstad et al., Bioinformatics, 19, 185-93, 2003; Irizarry et al., Nucleic Acids Res., 31, e15, 2003) as implemented in R (R Development Core Team, R foundation for statistical computing, Vienna, 2007) and Bioconductor (Gentleman et al., Genome Biology, 5, R80, 2004). Differentially expressed genes were identified using the permutation-based method of Tusher et al. (Proc. Natl. Acad. Sci. USA, 98, 5116-21, 2001) (sam) as implemented in the "samr" R package, using the median false discovery rate over 100 data permutations as a measure for statistical significance.
