if the DEseq package already installed?

Question

[zizigolu]

Hi friends

I opened rstudio I typed

> library("DESeq", lib.loc="/usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2")
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages
    'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-9.1   2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.

Attaching package: 'DESeq'

The following objects are masked from 'package:DESeq2':

    estimateSizeFactorsForMatrix, getVarianceStabilizedData,
    varianceStabilizingTransformation

> library("DESeq")

Is this packaged installed and ready to use?

Thank u

[Anton Shekhov]

The answer to your question is here http://stackoverflow.com/questions/4090169/elegant-way-to-check-for-missing-packages-and-install-them

And btw, you can install DESeq2, which contains all the functionality of the first version with extra features

[zizigolu]

I did like so but told

> installed.packages()[,"DEseq2"]
Error in installed.packages()[, "DEseq2"] : subscript out of bounds
> list.of.packages <- c("gDEseq2", "DEseq")
> new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"DEseq"])]
Error in list.of.packages %in% installed.packages()[, "DEseq"] : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in installed.packages()[, "DEseq"] : subscript out of bounds
> if(length(new.packages)) install.packages(new.packages)
Error in install.packages : 'match' requires vector arguments

[Anton Shekhov]

Probably the error in case-sensitivity of package name. You installed DESeq but searching for DEseq

The another approach to check is it installed - is just to call any function from this package. The function you can find in vignette. The solution I first showed is for automatic checking mostly

Answer 1

[Sean Davis]

Yes, the package is ready to use. However, you should be using DESeq2, not DESeq.

Answer 2

[Antonio R. Franco]

I don't see any problem

It seems that you have installed both, DESeq and DESeq2

The following objects are masked from ‘package:DESeq2’:

    estimateSizeFactorsForMatrix, getVarianceStabilizedData,
    varianceStabilizingTransformation

This means that you have the same functions, named the same way in both packages, and if loaded into R, the program does not know what to use. Since they are named tha same way, they are masked. You can decide which one to use writing any of these codes

DESeq::estimateSizeFactorsForMatrix() # or
DESeq2::estimateSizeFactorsForMatrix() # as examples

Other examples.. The function plotMDA is present in both limma and DESeq. If both are loaded into memory, you again need to decide in your code at the time of writing

limma::plotMDA() # or
DESeq2::plotMDA()

BTW, I agree witth both, Anton and the maintainer of DESeq versions: they recommend using DESeq2

[zizigolu]

thank you all, Sean and Antonio Anton

Answer 3

[Antonio R. Franco]

One more advice

You will see in Rstudio a check box in the package list. By hitting and marking these check boxes, you load and unload your packages. You don't need to run installed.packages() either, because RStudio will provide you with that list