Hello, I am having a merging issue with cytofkit version 1.2.4 run on R 3.2.4.
I am trying to run an analysis on couples of .fcs files. Unfortunately I cannot post the files as they are confidential.
Here's the code and the error message:
files <- list.files(path="C:/Users/data", pattern='.fcs$', full=TRUE)
paraFile <- list.files(path="C:/Users/data", pattern='.txt$', full=TRUE)
parameters <- as.character(read.table(paraFile, sep = "\t", header = TRUE)[, 1])
ID_047<-files[16:17]
merged_ID047<-cytof_exprsMerge(ID_047, markers=parameters,fixedNum = 500)
Error in y@f(x[, y@input]) :
Logicle Exception: DidNotConverge: scale() didn't converge
I can't figure out what is wrong. I have tried with the GUI with the same results. Can anybody help?
For completeness, here's the output of traceback()
10: .Call("logicle_transform", as.double(x), as.double(t), as.double(w),
as.double(m), as.double(a))
9: y@f(x[, y@input])
8: translist %on% `_data`
7: translist %on% `_data`
6: .local(`_data`, ...)
5: flowCore::transform(fcs, trans)
4: flowCore::transform(fcs, trans)
3: (function (fcsFile, comp = FALSE, verbose = FALSE, markers = NULL,
transformMethod = "auto_lgcl", scaleTo = NULL, w = 0.1, t = 4000,
m = 4.5, a = 0, q = 0.05)
{
name <- sub(".fcs", "", basename(fcsFile))
if (verbose) {
fcs <- read.FCS(fcsFile)
}
else {
fcs <- suppressWarnings(read.FCS(fcsFile))
}
if (comp == TRUE) {
if (comp && !is.null(fcs@description$SPILL)) {
fcs <- applyComp(fcs, "SPILL")
}
else if (comp && !is.null(fcs@description$SPILLOVER)) {
fcs <- applyComp(fcs, "SPILLOVER")
}
else if (comp && !is.null(fcs@description$COMP)) {
fcs <- applyComp(fcs, "COMP")
}
}
pd <- fcs@parameters@data
if (!(is.null(markers))) {
right_marker <- markers %in% pd$desc || markers %in%
pd$name
if (!(right_marker)) {
stop("\n Selected marker(s) is not in the input fcs files \n please check your selected markers! \n")
}
else {
desc_id <- match(markers, pd$desc)
name_id <- match(markers, pd$name)
mids <- c(desc_id, name_id)
marker_id <- unique(mids[!is.na(mids)])
}
}
else {
marker_id <- 1:ncol(fcs@exprs)
}
if (transformMethod == "auto_lgcl") {
trans <- auto_lgcl(fcs, channels = colnames(fcs@exprs)[marker_id])
transformed <- flowCore::transform(fcs, trans)
exprs <- transformed@exprs[, marker_id]
}
else if (transformMethod == "fixed_lgcl") {
trans <- flowCore::logicleTransform(w = w, t = t, m = m,
a = a)
exprs <- apply(fcs@exprs[, marker_id], 2, trans)
}
else if (transformMethod == "arcsin") {
trans <- flowCore::arcsinhTransform(a = 1, b = 1, c = 1)
exprs <- apply(fcs@exprs[, marker_id], 2, trans)
}
else if (transformMethod == "biexp") {
trans <- flowCore::biexponentialTransform(a = 0.5, b = 1,
c = 0.5, d = 1, f = 0, w = 0)
exprs <- apply(fcs@exprs[, marker_id], 2, trans)
}
else {
stop("transformMethod [", transformMethod, "] doesn't exist for cytofkit!")
}
if (!is.null(scaleTo)) {
exprs <- apply(exprs, 2, function(x) scaleData(x, scaleTo))
}
col_names <- paste0(pd$name, "<", pd$desc, ">")
colnames(exprs) <- col_names[marker_id]
row.names(exprs) <- paste(name, 1:nrow(exprs), sep = "_")
return(exprs)
})(dots[[1L]][[1L]], comp = FALSE, verbose = FALSE, markers = c("162Dy_CD45RA",
"164Dy_CD20", "166Er_CD33", "167Er_CD28", "168Er_CD24", "170Er_CD161",
"151Eu_CD38", "153Eu_CD11b", "155Gd_CCR6", "156Gd_CD94", "157Gd_CD86",
"158Gd_CXCR5", "160Gd_CCR7", "165Ho_CD127", "113In_CD57", "175Lu_HLADR",
"142Nd_CD19", "143Nd_CD4", "144Nd_CD8", "146Nd_IgD", "148Nd_CD11c",
"150Nd_CD3", "147Sm_CD85j", "149Sm_CD16", "152Sm_CD27", "154Sm_CD14",
"159Tb_CXCR3", "169Tm_ICOS", "171Yb_TCRgd", "172Yb_PD-1", "173Yb_CD123",
"174Yb_CD56", "176Yb_CD25"), transformMethod = "auto_lgcl", scaleTo = NULL,
w = 0.1, t = 4000, m = 4.5, a = 0, q = 0.05)
2: mapply(cytof_exprsExtract, fcsFiles, MoreArgs = list(comp = comp,
verbose = verbose, markers = markers, transformMethod = transformMethod,
scaleTo = scaleTo, w = w, t = t, m = m, a = a, q = q), SIMPLIFY = FALSE)
1: cytof_exprsMerge(ID_047, markers = parameters, fixedNum = 500)
Thanks
Margherita
