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