Question: error using the TTP package
gravatar for Bioinformatics
20 months ago by
Bioinformatics20 wrote:

I have tried to reproduce the example data provided by the author of TPP package 

resultPath = file.path(getwd(), 'Panobinostat_Vignette_Example')
trData <- tpptrImport(configTable=hdacTR_config, data=hdacTR_data)
normResults <- tpptrNormalize(data=trData)
trDataNormalized <- normResults[["normData"]]
load(file.path(resultPath, "dataObj", "fittedData.RData"), 
bNew <- 200
TRresultsBNew <- tpptrAnalyzeMeltingCurves(data=trDataFitted,
Error: could not find function "tpptrAnalyzeMeltingCurves"

The functions can be invoked from

At first it is missing " tpptrAnalyzeMeltingCurves" function 

Then after i manually invoke it from github, it is missing "retrieveDataFromESets_TR" function. again after invoking the function "eSetsToLongTable_fc" which consists of the above function. 

It is missing the "meltCurveParamNames" function. And then after adding this function manually, I get an error like  Starting melting curve analysis. Show Traceback Rerun with Debug

Error in `[.data.frame`(fDat, , cols1) : undefined columns selected 

what could be the reason for this?

ADD COMMENTlink modified 20 months ago by Martin Morgan ♦♦ 21k • written 20 months ago by Bioinformatics20
gravatar for Martin Morgan
20 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

Make sure that you are following the vignette corresponding to your version of the package. Do this by using

> browseVignettes(package="TPP")

from inside R.

If you are just starting out, make sure that you are using the current release version of R (version 3.3.0) and Bioconductor (version 3.3)

> R.version.string
[1] "R version 3.3.0 Patched (2016-06-09 r70752)"
> BiocInstaller::biocVersion()
[1] '3.3'

If you are not using the current version of R, then update to that first, and install the BiocInstaller and TPP packages as


Also make sure that you have not mixed package versions by executing the command


and following instructions to update or downgrade packages.

As you have seen, cutting and pasting the source code of the package into your R session is generally not an effective way to run the software.


ADD COMMENTlink modified 20 months ago • written 20 months ago by Martin Morgan ♦♦ 21k

@Martin Morgan the package is updated , I have done all these in advance.  I gave the same example as it is given by the author. so one can reproduce the error I obtained. 

ADD REPLYlink modified 20 months ago • written 20 months ago by Bioinformatics20

If I 


and then cut-and-paste your code I get

> load(file.path(resultPath, "dataObj", "fittedData.RData"), 
+     verbose=TRUE)
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '/home/mtmorgan/Panobinostat_Vignette_Example/dataObj/fittedData.RData', probable reason 'No such file or directory'

So unfortunately your example is not complete.

Fortunately, the vignettes in R packages are built dynamically, and the code is available in your installation. Here's how I can evaluate the vignette source in my R session

vig = vignette(package="TPP", "TPP_introduction")
source(file.path(vig$Dir, vig$R), echo=TRUE)

The entire code completes for me without problem. Also, I see that the function that you do not have is available

> head(tpptrAnalyzeMeltingCurves)
1 function (data, pValMethod = "maxQuant", pValFilter = list(minR2 = 0.8, 
2     maxPlateau = 0.3), pValParams = list(binWidth = 300))               
3 {                                                                       
4     message("Starting melting curve analysis.")                         
5     expInfo <- sapply(data, annotation)                                 
6     dataSplit <- retrieveDataFromESets_TR(data)       

The unusual thing that you say in your question is that "The functions can be invoked from" but one would never do that. Instead one would install and load the package

biocLite("TPP")  ## first time only

and proceed from there.

Here's my sessionInfo(), showing the version of R and other packages in my session after running the vignette. What is your session info?

> sessionInfo()
R version 3.3.0 Patched (2016-06-09 r70752)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
[1] gridExtra_2.2.1      TPP_2.2.3            ggplot2_2.1.0       
[4] openxlsx_3.0.0       Biobase_2.32.0       BiocGenerics_0.18.0 
[7] BiocInstaller_1.22.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5          knitr_1.13           magrittr_1.5        
 [4] splines_3.3.0        munsell_0.4.3        doParallel_1.0.10   
 [7] colorspace_1.2-6     foreach_1.4.3        stringr_1.0.0       
[10] plyr_1.8.4           tools_3.3.0          grid_3.3.0          
[13] gtable_0.2.0         nls2_0.2             lambda.r_1.1.7      
[16] futile.logger_1.4.1  iterators_1.0.8      digest_0.6.9        
[19] RColorBrewer_1.1-2   reshape2_1.4.1       bitops_1.0-6        
[22] futile.options_1.0.0 codetools_0.2-14     RCurl_1.95-4.8      
[25] VGAM_1.0-2           VennDiagram_1.6.17   labeling_0.3        
[28] stringi_1.1.1        compiler_3.3.0       scales_0.4.0        
[31] stats4_3.3.0         BiocStyle_2.1.7     


ADD REPLYlink modified 20 months ago • written 20 months ago by Martin Morgan ♦♦ 21k
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