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?
