Pipeline publication

[…] ss than 0.0001 were considered significant. The R script is available from ., For each group in each comparison the Pearson correlation coefficient for every transcript cluster was calculated in R using the mean probeset intensities for each group. The R code for the correlation coefficient analysis is available at: ., To test the significance of the difference between two correlation coefficients we used the web based tool at ., Annotation of significant probesets was obtained using the Affymetrix annotation files (HuEx-1_0-st-v2.na24.hg18.probeset.csv) available from the Affymetrix website. HTML results files with links to expression plots, X:MAP, Netaffx and NCBI were created in R., APT: Affymetrix Power Tools; FIRMA: Finding Isoforms using Robust Multichip, Average; LIMMA: Linear Models for Microarray Analysis; PLIER: Probe, Logarithmic Intensity Error; RMA: Robust Multi Average, SS developed the workflow, conceived the idea of the correlation coefficient and performed the data analysis. JP supervised the work. All authors read and approved the final manuscript., We would like to thank Dr. Michael Sadowski, Dr. Kevin Bryson and Anna Lobely for useful discussions.] […]

Pipeline specifications

Software tools APT, FIRMA, limma