Error in data.frame for limmaCtData function
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Entering edit mode
azmir004 • 0
@azmir004-17427
Last seen 5.8 years ago

Hi all,

I have a set of raw data from Taqman Low Density Array cards to be analysed with HTqPCR package. My data input has 2 types of files. First type of files are the .txt files for each sample which containing columns of 1) Flag (pass or fail), 2) Feature (name of genes), 3) Type (target or endogenous control), 4) Position (no. of wells), 5) Ct and 6) Sample (name of sample of respective file, e.g. treatment1). Second type of file is a .txt file containing columns of 1) File (name of file for each sample, e.g. treatment1.txt, treatment2.txt, control1.txt, control2.txt, ...), Phenotype (TREATMENT, CONTROL), Sample (number of sample, e.g. sample1, sample2, ...) and ID (name of samples, e.g. treatment1, treatment2, control1, control2, ...). I used the data that have been normalized using quantile normalization for limma test. The quantile-normalized data has been named as "q.norm". I encountered a problem while running limmaCtData function.  These are the R codes that I ran for limma test.

>design <- model.matrix(~0+phenotype)
>colnames(design) <- c("CONTROL", "TREATMENT")

>print(design)
>contrasts <- makeContrasts(TREATMENT-CONTROL, levels=design)
>colnames(contrasts) <- c("TREATMENT-CONTROL")
>print(contrasts)

>qDE.limma <- limmaCtData(q.norm, design=design, contrasts=contrasts)

The error warning came out after I ran limmaCtData function and it appeared as below:

> qDE.limma <- limmaCtData(q.norm, design=design, contrasts=contrasts)
Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 187, 0

This is the output of my traceback():

> traceback()
5: stop(gettextf("arguments imply differing number of rows: %s", 
       paste(unique(nrows), collapse = ", ")), domain = NA)
4: data.frame(..., check.names = FALSE)
3: cbind(deparse.level, ...)
2: cbind(rownames(res), featPos, res[, c("t", "P.Value", "adj.P.Val", 
       "logFC")], 2^(-res$logFC), both.means, both.cats)
1: limmaCtData(q.norm, design = design, contrasts = contrasts)

This is the output of my sessionInfo():

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows >= 8 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_Malaysia.1252 
[2] LC_CTYPE=English_Malaysia.1252   
[3] LC_MONETARY=English_Malaysia.1252
[4] LC_NUMERIC=C                     
[5] LC_TIME=English_Malaysia.1252    

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

other attached packages:
[1] HTqPCR_1.34.0       limma_3.36.3        RColorBrewer_1.1-2 
[4] Biobase_2.40.0      BiocGenerics_0.26.0

loaded via a namespace (and not attached):
 [1] gtools_3.8.1          bitops_1.0-6         
 [3] affy_1.58.0           stats4_3.5.1         
 [5] KernSmooth_2.23-15    BiocInstaller_1.30.0 
 [7] gplots_3.0.1          zlibbioc_1.26.0      
 [9] gdata_2.18.0          affyio_1.50.0        
[11] preprocessCore_1.42.0 tools_3.5.1          
[13] compiler_3.5.1        caTools_1.17.1.1

This is the output of my BiocInstaller::BiocValid():

> BiocInstaller::biocValid()

* sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows >= 8 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_Malaysia.1252 
[2] LC_CTYPE=English_Malaysia.1252   
[3] LC_MONETARY=English_Malaysia.1252
[4] LC_NUMERIC=C                     
[5] LC_TIME=English_Malaysia.1252    

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

other attached packages:
[1] HTqPCR_1.34.0       limma_3.36.3        RColorBrewer_1.1-2 
[4] Biobase_2.40.0      BiocGenerics_0.26.0

loaded via a namespace (and not attached):
 [1] gtools_3.8.1          bitops_1.0-6         
 [3] affy_1.58.0           stats4_3.5.1         
 [5] KernSmooth_2.23-15    BiocInstaller_1.30.0 
 [7] gplots_3.0.1          zlibbioc_1.26.0      
 [9] gdata_2.18.0          affyio_1.50.0        
[11] preprocessCore_1.42.0 tools_3.5.1          
[13] compiler_3.5.1        caTools_1.17.1.1     

Library path directories:
  C:/Users/Admin/Documents/R/win-library/3.5 

* Out-of-date packages
             Package       
DelayedArray "DelayedArray"
digest       "digest"      
later        "later"       
rtracklayer  "rtracklayer" 
snow         "snow"        
stringi      "stringi"     
xtable       "xtable"      
             LibPath                                     
DelayedArray "C:/Users/Admin/Documents/R/win-library/3.5"
digest       "C:/Users/Admin/Documents/R/win-library/3.5"
later        "C:/Users/Admin/Documents/R/win-library/3.5"
rtracklayer  "C:/Users/Admin/Documents/R/win-library/3.5"
snow         "C:/Users/Admin/Documents/R/win-library/3.5"
stringi      "C:/Users/Admin/Documents/R/win-library/3.5"
xtable       "C:/Users/Admin/Documents/R/win-library/3.5"
             Installed Built   ReposVer
DelayedArray "0.6.5"   "3.5.1" "0.6.6" 
digest       "0.6.16"  "3.5.1" "0.6.17"
later        "0.7.3"   "3.5.1" "0.7.5" 
rtracklayer  "1.40.5"  "3.5.1" "1.40.6"
snow         "0.4-2"   "3.5.0" "0.4-3" 
stringi      "1.1.7"   "3.5.0" "1.2.4" 
xtable       "1.8-2"   "3.5.1" "1.8-3" 
             Repository                                              
DelayedArray "https://bioconductor.org/packages/3.7/bioc/src/contrib"
digest       "https://cran.rstudio.com/src/contrib"                  
later        "https://cran.rstudio.com/src/contrib"                  
rtracklayer  "https://bioconductor.org/packages/3.7/bioc/src/contrib"
snow         "https://cran.rstudio.com/src/contrib"                  
stringi      "https://cran.rstudio.com/src/contrib"                  
xtable       "https://cran.rstudio.com/src/contrib"                  

update with biocLite()

Error: 7 package(s) out of date

As I am still new with R software, based on the information that I present here, can you help me where is my mistake and what should I do so I can run limmaCtData function?

software error limma data.frame • 771 views
ADD COMMENT
0
Entering edit mode
@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

I see that you've gone to a lot of effort to try to provide information, but I still can't guess what the problem is, particularly without seeing anything about your object q.norm.

You are using the HTqPCR package, so you need to attach the HTqPCR tag to your question, otherwise the HTqPCR authors may not be alerted to your question. The limmaCtData() is a HTqPCR function rather than a limma function. HTqPCR wraps limma functionality and it might be the wrapping that is causing the problem.

Alternatively you could use try using limma directly, which would allow me and others to provide more help.

 

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