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Question: Errors with HTqPCR v1.28.0 and BioC 3.4
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gravatar for julius
12 months ago by
julius20
United Kingdom
julius20 wrote:

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!

 

ADD COMMENTlink modified 10 months ago by henrik.seidel40 • written 12 months ago by julius20
1
gravatar for henrik.seidel
10 months ago by
henrik.seidel40 wrote:

See Subsetting qPCRset loses sample names, possibly due to change of assayDataElementReplace

ADD COMMENTlink written 10 months ago by henrik.seidel40
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