[BioC] HTqPCR, changeCtLayout is mislabeling the rows and is unable to return a qPCRset object

[Sam McInturf [guest]]

I am having problems reformatting my data.  My data has several samples on one plate, so I am reading in using the format = "plain" options, and then calling changeCtLayout() to reformat it.  I am reading in a 96 well plate that is organized as a 1x84 matrix (several wells not used).
For the sake of detail I will be very verbose, and the first few lines of my files are at the bottom of my post.

temp <- readCtData(file = "Plate1.txt", path = path, n.features = 84, n.data  =1, column.info = list(flag = 3, feature = 5, type = 4, Ct = 6, position =1), format = "plain", header = TRUE)

And this works well.  The vector that associates the features rows with samples is stored in a file read in by:

samples <- read.delim(myFile, header = TRUE, sep = "\t", stringsAsFactors = FALSE)[,"Sample"]
> head(samples)
[1] "Repl_d4" "Repl_d4" "Repl_d4" "Repl_d4" "Repl_d4" "Repl_d4"

I call:
changeCtLayout(temp, sample.order = samples)
Error in function (storage.mode = c("lockedEnvironment", "environment",  : 
  'AssayData' elements with different rowNames

Setting my qPCRset temp to 'q' and my samples vector to 'sample.order' and following the code for the changeCtLayout() function, I found that the error occurs when the rownames are assigned for the variables castnew, flagsnew, and Xnew when they are merged using the new("qPCRset", exprs...) function. 

>rownames(Xnew)
 [1] "Actin"   "EF"      "FRO3"    "FSD1"    "CSD1"    "FER4"    "Actin.1" "EF.1"    "FRO3.1"  "FSD1.1"  "CSD1.1"  "FER4.1" 
[13] "Actin.2" "EF.2"    "FRO3.2"  "FSD1.2"  "CSD1.2"  "FER4.2"  "FSD2"    "FSD2.1"  "FSD2.2"
>rownames(catsnew)
 [1] "Actin.1" "EF.1"    "FRO3.1"  "FSD1.1"  "CSD1.1"  "FER4.1"  "Actin.3" "EF.3"    "FRO3.3"  "FSD1.3"  "CSD1.3"  "FER4.3" 
[13] "Actin.5" "EF.5"    "FRO3.5"  "FSD1.5"  "CSD1.5"  "FER4.5"  "FSD2.6"  "FSD2.7"  "FSD2.8"

> all.equal(rownames(catsnew), rownames(flagsnew))
[1] TRUE

cats <- split(as.data.frame(featureCategory(q)), sample.order)
looking at the rows of the matrices in cats, all of the variable present in rownames(Xnew) and rownames(catsnew) are present. But when:
catsnew <- do.call("cbind", cats)
the rownames get mixed up.

Thank you for any and all help!

Samuel



the object temp
> temp
An object of class "qPCRset"
Size:  84 features, 1 samples
Feature types:            
Feature names:           Actin EF FRO3 ...
Feature classes:                  
Feature categories:      OK 
Sample names:                    Plate1 ...

> head(read.delim(myFile), 20)
   position     Sample   flag        type feature      Ct
1        A1    Repl_d4 Passed HouseKeeper   Actin 28.0867
2        A2    Repl_d4 Passed HouseKeeper      EF 20.8426
3        A3    Repl_d4 Passed         Exp    FRO3 21.7977
4        A4    Repl_d4 Passed         Exp    FSD1 16.0370
5        A5    Repl_d4 Passed         Exp    CSD1 17.4107
6        A6    Repl_d4 Passed         Exp    FER4 20.2024
7        A7 minusFe_d4 Passed HouseKeeper   Actin 29.3098
8        A8 minusFe_d4 Passed HouseKeeper      EF 23.0904
9        A9 minusFe_d4 Passed         Exp    FRO3 22.3609
10      A10 minusFe_d4 Passed         Exp    FSD1 22.8463
11      A11 minusFe_d4 Passed         Exp    CSD1 17.0752
12      A12 minusFe_d4 Passed         Exp    FER4 21.7814
13       B1    Repl_d4 Passed HouseKeeper   Actin 28.9077
14       B2    Repl_d4 Passed HouseKeeper      EF 28.5527
15       B3    Repl_d4 Passed         Exp    FRO3 22.6598
16       B4    Repl_d4 Passed         Exp    FSD1 17.5561
17       B5    Repl_d4 Passed         Exp    CSD1 18.9919
18       B6    Repl_d4 Passed         Exp    FER4 19.9053
19       B7 minusFe_d4 Passed HouseKeeper   Actin 28.9616
20       B8 minusFe_d4 Passed HouseKeeper      EF 22.0134




 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] HTqPCR_1.12.0      limma_3.14.3       RColorBrewer_1.0-5 Biobase_2.18.0     BiocGenerics_0.4.0

loaded via a namespace (and not attached):
 [1] affy_1.36.0           affyio_1.26.0         BiocInstaller_1.8.3   gdata_2.12.0          gplots_2.11.0        
 [6] gtools_2.7.0          preprocessCore_1.20.0 stats4_2.15.2         tools_2.15.2          zlibbioc_1.4.0  

--
Sent via the guest posting facility at bioconductor.org.