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Hi,
I am having trouble to work with qPCRset objects after subsetting them. In version 1.26.0 installed on my Linux machine (R 3.3.0;BioC 3.3) this works as expected:
library(HTqPCR)
exPath <- system.file("exData", package="HTqPCR")
exFiles <- read.delim(file.path(exPath, "files.txt"))
raw <- readCtData(files=exFiles$File, path=exPath)
raw_sub <- raw[,1:3]
colnames(raw)
#[1] "sample1" "sample2" "sample3" "sample4" "sample5" "sample6"
colnames(raw_sub)
#[1] "sample1" "sample2" "sample3"
sampleNames(raw_sub) <- LETTERS[1:3]
sampleNames(raw_sub)
#[1] "A" "B" "C"
sessionInfo()
# R version 3.3.0 (2016-05-03)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: CentOS Linux 7 (Core)
#
# locale:
# [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8
# [4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
# [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
# [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
#
# attached base packages:
# [1] parallel stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] HTqPCR_1.26.0 limma_3.28.21 RColorBrewer_1.1-2 Biobase_2.32.0
# [5] BiocGenerics_0.18.0
#
# loaded via a namespace (and not attached):
# [1] gtools_3.5.0 bitops_1.0-6 affy_1.50.0
# [4] stats4_3.3.0 KernSmooth_2.23-15 BiocInstaller_1.22.3
# [7] gplots_3.0.1 zlibbioc_1.18.0 gdata_2.17.0
# [10] affyio_1.42.0 preprocessCore_1.34.0 tools_3.3.0
# [13] caTools_1.17.1
However on my windows laptop (R 3.3.1;bioC 3.4) it doesn't work with version 1.26, 1.28 or 1.29 (devel):
library(HTqPCR)
exPath <- system.file("exData", package="HTqPCR")
exFiles <- read.delim(file.path(exPath, "files.txt"))
raw <- readCtData(files=exFiles$File, path=exPath)
raw_sub <- raw[,1:3]
colnames(raw)
#[1] "sample1" "sample2" "sample3" "sample4" "sample5" "sample6"
colnames(raw_sub)
#[1] "1" "2" "3"
sampleNames(raw_sub) <- LETTERS[1:3] # same result with colnames<-
# Error in (function (od, vd) :
# object and replacement value dimnames differ
# 10.
# stop("object and replacement value dimnames differ")
# 9.
# (function (od, vd)
# {
# if (is.null(vd))
# od <- seq_along(od) ...
# 8.
# mapply(FUN = f, ..., SIMPLIFY = FALSE)
# 7.
# Map(function(od, vd) {
# if (is.null(vd))
# od <- seq_along(od)
# else if (!setequal(od, vd)) ...
# 6.
# .validate_assayDataElementReplace(obj, value)
# 5.
# assayDataElementReplace(object, "exprs", value, validate = TRUE)
# 4.
# `exprs<-`(`*tmp*`, value = structure(c(11.463166, 33.949196,
# 27.956657, 26.92745, 24.992647, 11.280299, 26.921848, 35.940277,
# 40, 23.928349, 11.970958, 19.977112, 25.978376, 40, 31.980715,
# 28.956345, 26.925201, 32.985897, 26.959076, 26.976776, 31.92505, ...
# 3.
# `exprs<-`(`*tmp*`, value = structure(c(11.463166, 33.949196,
# 27.956657, 26.92745, 24.992647, 11.280299, 26.921848, 35.940277,
# 40, 23.928349, 11.970958, 19.977112, 25.978376, 40, 31.980715,
# 28.956345, 26.925201, 32.985897, 26.959076, 26.976776, 31.92505, ...
# 2.
# `sampleNames<-`(`*tmp*`, value = c("A", "B", "C"))
# 1.
# `sampleNames<-`(`*tmp*`, value = c("A", "B", "C"))
sampleNames(raw_sub)
#[1] "1" "2" "3"
sessionInfo()
# R version 3.3.1 (2016-06-21)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 7 x64 (build 7601) Service Pack 1
#
# locale:
# [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
# [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
# [5] LC_TIME=English_United Kingdom.1252
#
# attached base packages:
# [1] parallel stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] HTqPCR_1.28.0 limma_3.30.2 RColorBrewer_1.1-2 Biobase_2.34.0
# [5] BiocGenerics_0.20.0
#
# loaded via a namespace (and not attached):
# [1] gtools_3.5.0 bitops_1.0-6 affy_1.52.0 stats4_3.3.1
# [5] KernSmooth_2.23-15 BiocInstaller_1.24.0 gplots_3.0.1 zlibbioc_1.20.0
# [9] gdata_2.17.0 affyio_1.44.0 preprocessCore_1.36.0 tools_3.3.1
# [13] caTools_1.17.1
Thank you!
