"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
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jbgnielson • 0
@b2c61d6b
Last seen 5 weeks ago
United Kingdom

Hi all, currently trying to download gene expression data to run clustering analysis on it. I am following the instruction in this page " http://127.0.0.1:19589/library/ctsGE/doc/ctsGE.html ". I have my corresponding GSE as the one on that page also doesn't seem to work. When I try to build the expression matrix from the list of matrices: using the function "readTSGE", it states that the function could not be found. I am trying to see if i can import the function as a package online. But as far as I realise it should already be in the package ctsGE. Any help in this would be greatly appreciated

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("ctsGE")
BiocManager::install("bioassayR")
BiocManager::install("Biobase")
BiocManager::install("GEOquery")
library(GEOquery)
gse21193 <- getGEO('GSE21193')
gseAssays <- Biobase::assayData(gse21193)
gseExprs <- Biobase::assayDataElement(gseAssays[[1]][,c(1:10)],'exprs')
gseList <- lapply(1:10,function(x){data.frame(Genes = rownames(gseExprs),Value = gseExprs[,x])}) 
names(gseList) <- colnames(gseExprs)
data_dir <- system.file("extdata", package = "ctsGE")
files <- dir(path=data_dir,pattern = "\\.xls$")
rts <- readTSGE(gseList, labels = c("a","b","c","d","e","f","g","h","i","j") )

...Error in readTSGE(gseList, labels = c("a", "b", "c", "d", "e", "f", "g",  : 
  could not find function "readTSGE"
GeneExpression Clustering ctsGE • 429 views
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@james-w-macdonald-5106
Last seen 10 hours ago
United States

You have to load the library containing the function you want for it to be available.

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To further on James's comment: You installed the package with BiocManager::install("ctsGE") but you never loaded the package per the code shown library(ctsGE)

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Ah what a silly mistake. Thanks so much

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