SAS Macros for Microarray analysis
These are SAS macros written
in the McIntyre
Lab.
Name:
find_off
Description:
Uses negative controls to determine spot detection threshold.
Intended Platform: Agilent (2 dye arrays)
Data Format: Stacked
Author:
Lisa Bono
Name:
expression_means
Description:
Calculates the means of the signal intensities for the treatments.
Intended Platform: Agilent (2 dye arrays)
Data Format: Stacked
Author:
Lisa Bono
Name:
fdr
Description:
Labels p-values which have met specific FDR thresholds.
Intended Platform: Agilent (2 dye arrays)
Data Format:
Stacked
Author:
Lisa Bono
Name:
normalize
Description:
Normalizes and/or transforms signal intensities.
Intended Platform: Agilent (2 dye arrays)
Data Format:
Stacked
Author:
Lisa Bono
Name: perm_pvalue_multi_probes
Description: Calculates the p-values from data from real
and permuted ANOVA results of multiple probes.
Intended Platform: Agilent (2 dye arrays)
Data Format:
Stacked
Author: Lisa Bono
Name: QC_slide_macro
Description: Calculates basic statistics and creates a
density plot for the negative controls and genes of both dyes.
Intended Platform: Agilent (2 dye arrays)
Data Format: Side by side
Author: Lisa Bono
Name: percent_off
Description: Calculates the percent of the time a gene or
feature is off based on the Affy P,M,A designation.
Intended Platform: Affymetrix (single
dye arrays)
Data Format:
side by side
Author: Laura A.
Higgins, Ph.D.
Name: quartile_maker
Description: Calculates the quartile that a signal is ranked in for a gene or feature.
Intended Platform: Affymetrix (single dye arrays)
Data Format:
side by side
Author: Laura A.
Higgins, Ph.D.
Name: kappa_table
Description: Creates a table of simple and weighted Kappa statistics based on the percent_off and quartile of a P,M,A or signal values between a pair of chips.
Intended Platform: Affymetrix (single dye arrays)
Data Format:
side by side
Author: Laura A.
Higgins, Ph.D.
Name: stacker
Description: Takes side by side format data of 2 chips and
stacks them on top of one another, producing a “Stacked” data format.
Intended Platform: Affymetrix (single dye arrays)
Data Format:
side by side
Author: Laura A.
Higgins, Ph.D.
Definitions for specific
terms referred to in the macro files can be found here.