Package: AgiMicroRna; Error in Loading the file
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@neelakandanbt-14048
Last seen 5.2 years ago
National Institute of Technology

hello evryone,

  I was trying to analyse a group of agilent Microrarray data that was. i was using the AgiMicroRna package for this.

but when i was load the input file to the command it as showing the following errors.

1)i was using the following commands

while loading the package it was showing that few packages could not be loaded

library("AgiMicroRna")
Loading required package: affycoretools
Error: package or namespace load failed for ‘affycoretools’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘S4Vectors’
Error: package ‘affycoretools’ could not be loaded

 

2) when trying to load the input file it was showing the following error

> atargets.micro<-readTargets(infile="targets.txt",verbose=TRUE)


Error in read.table(file, header = TRUE, stringsAsFactors = FALSE, sep = sep,  : 
  unused arguments (infile = "targets.txt", verbose = TRUE)

Kindly help me in this.

 

AgiMicroRna • 719 views
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Axel Klenk ▴ 990
@axel-klenk-3224
Last seen 18 hours ago
Switzerland

Dear neelakandanbt,

the first message indicates that package 'S4Vectors' is not installed.  You need to install it before you can continue.

Please follow the instructions here:

https://bioconductor.org/install/

on how to install Bioconductor packages.  I'd expect the second issue to go away once the first is fixed.

How did you install package 'AgiMicroRna' ?? -- If you had followed the instructions above I'd expect the dependencies

to be installed for you as well.

Hope this helps,

 - axel

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@neelakandanbt-14048
Last seen 5.2 years ago
National Institute of Technology
dear Axel Klenk,  Thanks for the support. I was downloading the AgiMicroRna package using the command ``` source("https://bioconductor.org/biocLite.R") biocLite("AgiMicroRna")``` even then it showed the error on installing the package. That the package Affycoretools was not instaled so I installed the Affycoretools package seperately from the bioconductor. now it is working well.  
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