Hi,

I?m using the gosummaries() function on an eBayes() MArrayLM object. All is well down to lfc = log2(1.35), using the following expression:

GOsum1 <- gosummaries(efit, p.value = 0.05, lfc = log2(1.35), go_branches = c("BP"), min_set_size = 5, max_set_size = 1000, adjust.method = "fdr", exp = NULL, annotation = NULL, components = c(1), max_signif = 40, show_genes = FALSE, n_genes = 30, organism = "hsapiens")

Resulting in the following number of genes:
G1 > G2: 4128
G1 < G2: 1945

However, attempting the analysis on lfc = log2(1.3) gave the following error: Error in function (type, msg, asError = TRUE)  : Empty reply from server.

My intention was to analyze the data using lfc = log2(1.25), since this fold change give interesting results using the enrichPathway() function of the ReactomePA package.

Many thanks for any help and guidance.