Hello,
I would like your suggestions for this error with rma() function, for analysing microRNA-affymetrix data. I downloaded the package cdf (miRNA-4_0-st-v1_CDF) (provided below), created the package with make.cdf.package, installed it with R CMD INSTALL.
library(makecdfenv)
make.cdf.package(filename = "miRNA-4_0-st-v1.cdf",
packagename = "miRNA-4_0-st-v1.cdf",
cdf.path = "./miRNA_4_0_CDF/",
package.path= "/shared/home/mkondili/Tools_Packages/",
compress = FALSE,
species = "Mus_musculus")
Actually during installation, I get a warning :
R CMD INSTALL miRNA-4_0-st-v1.cdf
* installing to library ‘/shared/ifbstor1/home/mkondili/R/x86_64-conda-linux-gnu-library/4.1’
* installing *source* package ‘mirna40cdf’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘mirna40cdf’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘mirna40cdf’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘mirna40cdf’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘mirna40cdf’
Warning in data(list = pkgname, package = pkgname, envir = where) :
data set ‘mirna40cdf’ not found
But ,in the main script ,the library is well installed :
library(mirna40cdf )
"mirna40cdf" %in% installed.packages()
[1] TRUE
But, when I run :
Data <- ReadAffy(cdfname="mirna40cdf")
Data %>% glimpse
Formal class 'AffyBatch' [package "affy"] with 10 slots
..@ cdfName : chr "mirna40cdf"
..@ nrow : Named int 541
.. ..- attr(*, "names")= chr "Rows"
..@ ncol : Named int 541
.. ..- attr(*, "names")= chr "Cols"
..@ assayData :<environment: 0x55fb8e1cb1a0>
eset.rma <- affy::rma(Data)
I get the following error:
Error in get(cdfname, envir = as.environment(paste("package:", cdfname,
object 'mirna40cdf' not found
A previous post has been resolved on the same error, but it is of a very old R.version. (Error in get(cdfname, object 'mm430mmentrezgcdf' not found)
I would like to find where is this line found (get(cdfname)..) ,and why it is not finding the mirna40cdf object. Maybe I should correct sth during the installation process?
sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] makecdfenv_1.70.0 affyio_1.64.0 lubridate_1.9.2 forcats_1.0.0 dplyr_1.1.2 purrr_1.0.1
[7] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2 tidyverse_2.0.0 stringr_1.5.0
[13] limma_3.50.0 affy_1.72.0 Biobase_2.54.0 BiocGenerics_0.40.0
loaded via a namespace (and not attached):
[1] pillar_1.9.0 compiler_4.1.1 BiocManager_1.30.18 tools_4.1.1 zlibbioc_1.40.0 timechange_0.2.0
[7] lifecycle_1.0.3 preprocessCore_1.56.0 gtable_0.3.3 pkgconfig_2.0.3 rlang_1.1.1 cli_3.6.1
[13] rstudioapi_0.15.0 xfun_0.39 knitr_1.43 withr_2.5.0 generics_0.1.3 vctrs_0.6.3
[19] hms_1.1.3 grid_4.1.1 tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.4
[25] tzdb_0.4.0 magrittr_2.0.3 scales_1.2.1 colorspace_2.1-0 utf8_1.2.3 stringi_1.7.12
[31] munsell_0.5.0
The package in zip file can be retrieved here:
https://github.com/mariakondili/microRNA_affy_analysis/blob/main/miRNA-4_0-st-v1_CDF.zip
