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

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

data("hdacTR_smallExample")
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"), 
    verbose=TRUE)
bNew <- 200
TRresultsBNew <- tpptrAnalyzeMeltingCurves(data=trDataFitted,
    pValParams=list(binWidth=bNew,minR2=0.8,maxPlateau=0.3))
Error: could not find function "tpptrAnalyzeMeltingCurves"

The functions can be invoked from https://github.com/Bioconductor-mirror/TPP/tree/master/R

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?

tpp
ADD COMMENTlink modified 17 months ago by Martin Morgan ♦♦ 20k • written 17 months ago by Bioinformatics20
0
gravatar for Martin Morgan
17 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k 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

source("https://bioconductor.org/biocLite.R")
biocLite("TPP")

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

BiocInstaller::biocValid()

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 17 months ago • written 17 months ago by Martin Morgan ♦♦ 20k

@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 17 months ago • written 17 months ago by Bioinformatics20

If I 

library(TPP)

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 https://github.com/Bioconductor-mirror/TPP/tree/master/R" but one would never do that. Instead one would install and load the package

source("https://bioconductor.org/biocLite.R")
biocLite("TPP")  ## first time only
library(TPP)

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

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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 17 months ago • written 17 months ago by Martin Morgan ♦♦ 20k
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