diffExpr returns a DEG table with fold changes and p-values and an image containing 2 tables, one showing the breakdown of number of samples used in the analysis and a summary table for number of differentially expressed genes (DEG) given manually set fold-change and p-value thresholds.
diffExpr(
object,
analysis.type,
groups,
group.col,
regions,
region.col,
slide.col = "slide_name",
element = "q_norm",
multi.core = TRUE,
n.cores = 1,
p.adjust = "fdr",
pairwise = TRUE,
fc.lim = 1.2,
pval.lim.1 = 0.05,
pval.lim.2 = 0.01
)Name of the NanoStringGeoMxSet to perform DE analysis on
Analysis type either "Between Groups" or "Within Groups"
One or more groups of interest (needs to be variables within group.col)
Column for group (groups are usually found in different slides)
One or more regions of interest (needs to be variables within region.col)
Column for region (regions are usually found within a slide)
Column for slide name (default is "slide name")
assayDataElement of the geoMxSet object to run the DE on
Set to TRUE to use multicore, FALSE to run in cluster mode (default is TRUE)
Number of cores to use, set to 1 if running in serial mode (default is 1)
Method to use for pvalue adjustment. Choices are "holm", "hochberg","hommel","bonferroni","BH","BY","fdr","none". (default is "BH")
Boolean to calculate least-square means pairwise differences (default is TRUE)
Fold Change limit for summarizing genes of interest (default is 1.2)
P-value limit for summarizing differentially expressed (DEG) genes, usually more stringent (default is 0.05)
P-value limit for summarizing differentially expressed (DEG) genes, usually more lenient (default is 0.10)
a list containing mixed model output data frame, grid tables for samples used in analysis and summary of significant genelists
This function will run mixedModelDE from the GeoMxTools package.