Hi,

 

I originally had problems installing Affy on R version 2.10.1 (while
learning to use Limma), read various threads on Affy installation issues and
potential version incompatibilities, and decided to reinstall R from
scratch, after deleting all previous versions.

 

Now, when I follow Bioconductor installing instructions, I get the message
below.

 

> source("http://bioconductor.org/biocLite.R")

> biocLite()

Using R version 2.10.1, biocinstall version 2.5.10.

Installing Bioconductor version 2.5 packages:

 [1] "affy"         "affydata"     "affyPLM"      "annaffy"      "annotate"


 [6] "Biobase"      "biomaRt"      "Biostrings"   "DynDoc"       "gcrma"


[11] "genefilter"   "geneplotter"  "hgu95av2.db"  "limma"        "marray"


[16] "multtest"     "vsn"          "xtable"       "affyQCReport"

Please wait...

 

Error in read.dcf(file = tmpf) : 

  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!

****

 

Now, even the Limma library is not installed. 

 

What is this problem and how do I fix it? 

 

Marissa LaMadrid

Sound Choice Pharmaceutical Institute

Seattle, WA


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