Error in systemPipeR

Hi,

I am trying systemPipeR manual. In the very beginning I get following error. I don't know what to do. Any help is appreciated.

Thanks!

source("systemPipeRNAseq_Fct.R")
Error in file(filename, "r", encoding = encoding) :
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'systemPipeRNAseq_Fct.R': No such file or direc

r systempiper

• 3,413 views • link

updated 3.4 years ago by Ram

• written 11.5 years ago by Parham

1 answer

Looks like you might not have the R script in your working directory. You can setwd() to the dir that contains the script, or copy it over to your working directory and then try again.

Also, doesn't look like your line is in the manual here

• 0 views • link

written 11.5 years ago by Ram

It doesn't say where this script is placed! Therefore I have no clue how to set the directory to it or copy it!

It's from section 2.2. from this manual if you could have a look please.

Thanks!

• 0 views • link

updated 4.3 years ago by Ram

• written 11.5 years ago by Parham

You don't need to do both library() and source(). Use the link I gave you to install systempipeR and then run library(), that should work.

The source() is only if you have any custom functions to load.

• 0 views • link

written 11.5 years ago by Ram

Oh thanks! I was doing both, now I skip source().

• 0 views • link

updated 4.3 years ago by Ram

• written 11.5 years ago by Parham

More posts like this

scRNAseq error source a custom function
written 3.1 years ago by camillab. •

Hi, Apologies if it is a stupid error/common knowledge! I am trying to integrate two scRNAseq datasets and I am following [this tutorial][1] and I …
EQTL MATRIX _EQTL
written 4.6 years ago by Nai •

```r setwd("C:/Users/genetics/Desktop/Plant_39/eqtl/") getwd() [1] "C:/Users/genetics/Desktop/Plant_39/eqtl" library(MatrixEQTL) base.dir = find.package("MatrixEQTL") useModel = modelLINEAR SNP_file_name = paste(base.dir, "SNP.txt", sep="") expression_file_name = paste(base.dir, "GE.txt", sep="") covariates_file_name = character() …
Weird error in R
written 7.8 years ago by Za

Hi, Sorry, whatever I am trying R in installing some package, I am getting this error Any suggestion please? > source("https://bioconductor.org/biocLite.R") Error in file(filename, "r", …
Bioconductor not re-installing
written 9.9 years ago by theaspirant •

Hello everyone, I am new to this area, I installed R some days back and then Bioconductor package, at the time of installing many other …
How to set up TCGAbiolinks in R studio?
written 10.2 years ago by elizabethR

Hey I am trying to set up TCGABiolinks in R studio, starting by downloading and collating data and then doing differential expression analysis of RNASeq …
Query For biocLite
written 10.2 years ago by viswanathrana29 •

Hi all I heave insatlled then i install Bioconductor Packages through this command ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite() in …
R program (bioconductor)
written 11.4 years ago by bioinfo

Hi While I was connecting the bioconductor packages I got an error ``` source ("http://www.bioconductor.org/biocLite.R") Error in file(filename, "r", encoding = encoding) : cannot open …
sciClone error with analysis
written 12.2 years ago by cristinam09 •

I manage to run the sciClone script with the demo data from github. I now have the following error message after I ask to `writeClusterTable(sc, …
How To Solve The Read.Maimages Error In Limma Package Of R ?
written 12.8 years ago by Arpitha Hebbar

i'm working on agilent data. for the analysis i am using R and bioconductor package limma. in read.maimages RG <-read.maimages(targets$FileName,source="agilent") m getting the following error …
Problem In Connecting Cran R Site
written 13.3 years ago by Nitin

Hello, I m trying to install R packages via CRAN mirror sites..But i am getting Following error <pre><code>Type 'demo()' for some demos, 'help()' for on-line …