"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
1
0
Entering edit mode
jbgnielson • 0
@b2c61d6b
Last seen 7 months 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 • 696 views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 4 hours ago
United States

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

1
Entering edit mode

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)

ADD REPLY
0
Entering edit mode

Ah what a silly mistake. Thanks so much

ADD REPLY

Login before adding your answer.

Traffic: 666 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6