library(tidyverse)

library(affyPLM)

library(AmpAffyExample)

data(AmpData)

sampleNames(AmpData) <- c("N1","Good Quality","Poor Quality","A1","A2","A3")

Pset1 <- fitPLM(AmpData)

pm.index <- unlist(affy::indexProbes(Pset1, "pm", row.names(coefs(Pset1))))

rows <- Pset1@nrow

cols <- Pset1@ncol

pm.x.locs <- pm.index %% rows

pm.x.locs[pm.x.locs == 0] <- rows

pm.y.locs <- pm.index %/% rows + 1

plm_resids <-

tibble::as_tibble(Pset1@residuals$PM.resid) %>%

mutate(

probe = rownames(Pset1@residuals$PM.resid),

x = pm.x.locs,

y = pm.y.locs

) %>%

pivot_longer(cols = c(1:6), names_to = "Sample", values_to = "Intensity") %>%

dplyr::filter(Sample %in% c("Good Quality", "Poor Quality"))

save(plm_resids, file = "RData/plm_resids.RData")