Dear authors
Thank you for developing such an excellent package！
When I use it,I met some questions.
Because all the cells were filtered out when I first run the original code, three places in the original code were commented：
Then I am encountering errors on "step 4: measuring baselines ..."：
Error in mixtools::normalmixEM(data.c, lambda = rep(1, 3)/3, mu = c(-0.2, : NA/NaN/Inf in foreign function call (arg 4)
but I have checked that there is no NA value in my counts. Is it generated in the process of calculation? I can't solve this problem .Could you please help me?
I would appreciate it if you could reply to me.
Thank you very much!
Dear authors Thank you for developing such an excellent package！ When I use it,I met some questions. Because all the cells were filtered out when I first run the original code, three places in the original code were commented：
1—— `# genes.raw <- apply(rawmat, 2, function(x) (sum(x > 0)))
if (sum(genes.raw > 200) == 0)
stop("none cells have more than 200 genes")
if (sum(genes.raw < 100) > 1) {
rawmat <- rawmat[, -which(genes.raw < 200)]
print(paste("filtered out ", sum(genes.raw <= 200),
" cells with less than 200 genes; remaining ", ncol(rawmat),
" cells", sep = ""))
}
2——
if (length(toRev) > 0) {
anno.mat <- anno.mat[-toRev, ]
}
ToRemov2 <- NULL
for (i in 8:ncol(anno.mat)) {
cell <- cbind(anno.mat$chromosome_name, anno.mat[, i])
cell <- cell[cell[, 2] != 0, ]
if (length(as.numeric(cell)) < 5) {
rm <- colnames(anno.mat)[i]
ToRemov2 <- c(ToRemov2, rm)
}
else if (length(rle(cell[, 1])$length) < 23 | min(rle(cell[,
1])$length) < ngene.chr) {
rm <- colnames(anno.mat)[i]
ToRemov2 <- c(ToRemov2, rm)
}
i <- i + 1
}
if (length(ToRemov2) == (ncol(anno.mat) - 7))
stop("all cells are filtered")
if (length(ToRemov2) > 0) {
anno.mat <- anno.mat[, -which(colnames(anno.mat) %in%
ToRemov2)]
}
3——
ToRemov3 <- NULL
for (i in 8:ncol(anno.mat2)) {
cell <- cbind(anno.mat2$chromosome_name, anno.mat2[,
i])
cell <- cell[cell[, 2] != 0, ]
if (length(as.numeric(cell)) < 5) {
rm <- colnames(anno.mat2)[i]
ToRemov3 <- c(ToRemov3, rm)
}
else if (length(rle(cell[, 1])$length) < 23 | min(rle(cell[,
1])$length) < ngene.chr) {
rm <- colnames(anno.mat2)[i]
ToRemov3 <- c(ToRemov3, rm)
}
i <- i + 1
}
if (length(ToRemov3) == ncol(norm.mat.relat))
stop("all cells are filtered")
if (length(ToRemov3) > 0) {
norm.mat.relat <- norm.mat.relat[, -which(colnames(norm.mat.relat) %in%
ToRemov3)]
}`
Then I am encountering errors on "step 4: measuring baselines ..."：
Error in mixtools::normalmixEM(data.c, lambda = rep(1, 3)/3, mu = c(-0.2, : NA/NaN/Inf in foreign function call (arg 4)but I have checked that there is no NA value in my counts. Is it generated in the process of calculation? I can't solve this problem .Could you please help me? I would appreciate it if you could reply to me. Thank you very much!