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Question: Error in readPlateList
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gravatar for sil1
5 months ago by
sil10
sil10 wrote:

Hi, 

I have a problem with a script. It gives error at the very beginning at I really don't know why. I used the exact same one few months ago and it was working absolutely fine. Now I need to repeat the analyses and I can't. R software has been recently reinstalled and it is at its latest version.

All the files have the right name and are in the right directory.

I copied all the commands lines below.

Hope you can help me

Regards,

 

Silvia

 

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite("cellHTS2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘cellHTS2’
trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/cellHTS2_2.40.0.zip'
Content type 'application/zip' length 7092883 bytes (6.8 MB)
downloaded 6.8 MB

package ‘cellHTS2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\RNAi\AppData\Local\Temp\RtmpKEvvi3\downloaded_packages
Old packages: 'RSQLite'
Update all/some/none? [a/s/n]: library(cellHTS2)
Update all/some/none? [a/s/n]: a

  There is a binary version available but the source version is later:
        binary source needs_compilation
RSQLite  1.1-2    2.0              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/RSQLite_1.1-2.zip'
Content type 'application/zip' length 1996792 bytes (1.9 MB)
downloaded 1.9 MB

package ‘RSQLite’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\RNAi\AppData\Local\Temp\RtmpKEvvi3\downloaded_packages
> dataPath = "R:/Silvia Cirillo/R templates/"
> expName = "FITC-G3_TO_screen_new vesicles"
> outPath = paste(dataPath,"FITC-G3_TO_screen_new vesicles")
> confFile = file.path(dataPath,"SC_PlateConf2.txt")
> logFile = file.path(dataPath,"SC_screenlog2.txt")
> desFile = file.path(dataPath,"Description2.txt")
> geneIDs = file.path(dataPath,"TO_annotation.txt")
> posControls = "PLK1|MYO5A|MYO5B|MYO5C|CAV1|ARF6|RAB7|siGLO RED"
> negControls = "on target#1|on target#2"
> x <- readPlateList("SC_platelist2.txt", name = expName, path = dataPath)
Error in readPlateList("SC_platelist2.txt", name = expName, path = dataPath) : 
  could not find function "readPlateList"

ADD COMMENTlink written 5 months ago by sil10
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