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Original post failing:

I am trying to use HTqPCR to analyzer data from qPCR reactions set on three 384 plates (60 samples tested for 6 miRNAs in triplicates, 20 samples per plate tested on all 6 miRNAs). The configuration of the plate is different from array cards and I am having trouble getting the data imported using the default SDS format with readCtData followed by changeCtLayout.

The errors I get seem to suggest that the SDS format may not be amenable.

...

Here is what I tested:

>raw2 <- readCtData("/imppc/labs/lslab/share/data/raw_data/qPCR/qPCR_01/SDS_results/RT_qPCR_miRNA_01_plate1_2_3_180420.sdm-Result DataTableCentric.txt",
                   format="SDS",
                   n.features=1080,
                   n.data=1)

> show(raw2)
An object of class "qPCRset"
Size:  1080 features, 1 samples
Feature types:          
Feature names:         miR-24-3p miR-24-3p miR-24-3p ...
Feature classes:          
Feature categories:     OK, Undetermined
Sample names:         /imppc/labs/lslab/share/data/raw_data/qPCR/qPCR_01/SDS_results/RT_qPCR_miRNA_01_plate1_2_3_180420.sdm-Result DataTableCentric ...

>sampleNames(raw2)
[1] "/imppc/labs/lslab/share/data/raw_data/qPCR/qPCR_01/SDS_results/RT_qPCR_miRNA_01_plate1_2_3_180420.sdm-Result DataTableCentric"

>sample.order3<-c(rep(rep(c("1","2","3","4"),6),3),
                     rep(rep(c("5","6","7","8"),6),3),
                     rep(rep(c("9","10","11","12"),6),3),
                     rep(rep(c("13","14","15","16"),6),3),
                     rep(rep(c("17","18","19","20"),6),3),
                     rep(rep(c("21","22","23","24"),6),3),
                      rep(rep(c("25","26","27","28"),6),3),
                      rep(rep(c("29","30","31","32"),6),3),
                      rep(rep(c("33","34","35","36"),6),3),
                      rep(rep(c("37","38","39","40"),6),3),
                     rep(rep(c("41","42","43","44"),6),3),
                      rep(rep(c("45","46","47","48"),6),3),
                      rep(rep(c("49","50","51","52"),6),3),
                      rep(rep(c("53","54","55","56"),6),3),
                      rep(rep(c("57","58","59","60"),6),3))

> raw3<-changeCtLayout(raw2,sample.order=as.vector(sample.order20))
Error in (function (storage.mode = c("lockedEnvironment", "environment",  :
  'AssayData' elements with different rowNames

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /software/debian-8/general/R-3.4.2/lib/R/lib/libRblas.so
LAPACK: /software/debian-8/general/R-3.4.2/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=C                  LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=es_ES.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] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] doBy_4.5-15         data.table_1.10.4-3 drc_3.0-1           readr_1.1.1         readxl_1.0.0        HTqPCR_1.32.0      
 [7] limma_3.34.9        RColorBrewer_1.1-2  Biobase_2.38.0      BiocGenerics_0.24.0 qpcR_1.4-0          Matrix_1.2-12      
[13] robustbase_0.92-8   rgl_0.99.9          minpack.lm_1.2-1    MASS_7.3-49        

loaded via a namespace (and not attached):
 [1] jsonlite_1.5          splines_3.4.2         gtools_3.5.0          shiny_1.0.5           assertthat_0.2.0     
 [6] affy_1.56.0           stats4_3.4.2          cellranger_1.1.0      pillar_1.1.0          lattice_0.20-35      
[11] quantreg_5.35         digest_0.6.15         minqa_1.2.4           colorspace_1.3-2      sandwich_2.4-0       
[16] plyr_1.8.4            htmltools_0.3.6       httpuv_1.3.5          preprocessCore_1.40.0 pkgconfig_2.0.1      
[21] SparseM_1.77          zlibbioc_1.24.0       xtable_1.8-2          mvtnorm_1.0-7         scales_0.5.0         
[26] gdata_2.18.0          affyio_1.48.0         lme4_1.1-15           MatrixModels_0.4-1    tibble_1.4.2         
[31] mgcv_1.8-23           car_2.1-6             TH.data_1.0-8         nnet_7.3-12           pbkrtest_0.4-7       
[36] cli_1.0.0             survival_2.41-3       magrittr_1.5          crayon_1.3.4          mime_0.5             
[41] nlme_3.1-131.1        gplots_3.0.1          BiocInstaller_1.28.0  tools_3.4.2           hms_0.4.1            
[46] multcomp_1.4-8        munsell_0.4.3         plotrix_3.7           compiler_3.4.2        caTools_1.17.1       
[51] rlang_0.2.0           grid_3.4.2            nloptr_1.0.4          rstudioapi_0.7        htmlwidgets_1.0      
[56] crosstalk_1.0.0       bitops_1.0-6          codetools_0.2-15      R6_2.2.2              zoo_1.8-1            
[61] knitr_1.20            utf8_1.1.3            KernSmooth_2.23-15    Rcpp_0.12.15          DEoptimR_1.0-8   

Thank you,

Lauro