Errors with HTqPCR v1.28.0 and BioC 3.4
1
2
Entering edit mode
julius ▴ 20
@julius-7000
Last seen 6.5 years ago
United Kingdom

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!

 

HTqPCR • 1.4k views
ADD COMMENT
1
Entering edit mode
ADD COMMENT

Login before adding your answer.

Traffic: 560 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6