R help - May 2009 - 'RG' looks like a pre-2.4.0 S4 object: please recreate it

I would like to load ApoAI.RData. During the operation of reading this 
data an error occurs. There is also a problem with STF file.

 > library (limma)
 > load("ApoAI.RData")
Warning message:
'RG' looks like a pre-2.4.0 S4 object: please recreate it
 > objects()
[1] "RG"
 > names(RG)
[1] "R"       "G"       "Rb"      "Gb"  
"printer" "genes"   "targets"
 > RG$targets
      FileName  Cy3      Cy5
c1 a1koc1.spot Pool  C57BL/6
c2 a1koc2.spot Pool  C57BL/6
c3 a1koc3.spot Pool  C57BL/6
c4 a1koc4.spot Pool  C57BL/6
c5 a1koc5.spot Pool  C57BL/6
c6 a1koc6.spot Pool  C57BL/6
c7 a1koc7.spot Pool  C57BL/6
c8 a1koc8.spot Pool  C57BL/6
k1 a1kok1.spot Pool ApoAI-/-
k2 a1kok2.spot Pool ApoAI-/-
k3 a1kok3.spot Pool ApoAI-/-
k4 a1kok4.spot Pool ApoAI-/-
k5 a1kok5.spot Pool ApoAI-/-
k6 a1kok6.spot Pool ApoAI-/-
k7 a1kok7.spot Pool ApoAI-/-
k8 a1kok8.spot Pool ApoAI-/-
 > spottypes=readSpotTypes("ApoAISpotTypes.txt")
 > spottypes
  SpotType      ID Name  Color
1     cDNA       *    *  black
2    BLANK   BLANK    *  brown
3    Blank   Blank    * orange
4  Control Control    *   blue
 > RG$genes$Status=controlStatus(spottypes, RG)
Matching patterns for: 
Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), 
nrow = nr,  :
  attempt to set an attribute on NULL

Thank you for your help.

Regars,
B.

supply result of sessionInfo() -- undoubtedly you have outdated packages
installed.  to work with the current image and get efficient support from
this
list, use R 2.9 and install packages using biocLite. do not cross-post to
r-help.

On Wed, May 6, 2009 at 12:53 PM, Barbara Cegielska
<barceg@ibch.poznan.pl>wrote:
> I would like to load ApoAI.RData. During the operation of reading this data
> an error occurs. There is also a problem with STF file.
>
> > library (limma)
> > load("ApoAI.RData")
> Warning message:
> 'RG' looks like a pre-2.4.0 S4 object: please recreate it
> > objects()
> [1] "RG"
> > names(RG)
> [1] "R"       "G"       "Rb"     
"Gb"      "printer" "genes"   "targets"
> > RG$targets
>     FileName  Cy3      Cy5
> c1 a1koc1.spot Pool  C57BL/6
> c2 a1koc2.spot Pool  C57BL/6
> c3 a1koc3.spot Pool  C57BL/6
> c4 a1koc4.spot Pool  C57BL/6
> c5 a1koc5.spot Pool  C57BL/6
> c6 a1koc6.spot Pool  C57BL/6
> c7 a1koc7.spot Pool  C57BL/6
> c8 a1koc8.spot Pool  C57BL/6
> k1 a1kok1.spot Pool ApoAI-/-
> k2 a1kok2.spot Pool ApoAI-/-
> k3 a1kok3.spot Pool ApoAI-/-
> k4 a1kok4.spot Pool ApoAI-/-
> k5 a1kok5.spot Pool ApoAI-/-
> k6 a1kok6.spot Pool ApoAI-/-
> k7 a1kok7.spot Pool ApoAI-/-
> k8 a1kok8.spot Pool ApoAI-/-
> > spottypes=readSpotTypes("ApoAISpotTypes.txt")
> > spottypes
>  SpotType      ID Name  Color
> 1     cDNA       *    *  black
> 2    BLANK   BLANK    *  brown
> 3    Blank   Blank    * orange
> 4  Control Control    *   blue
> > RG$genes$Status=controlStatus(spottypes, RG)
> Matching patterns for: Error in matrix(unlist(value, recursive = FALSE,
> use.names = FALSE), nrow = nr,  :
>  attempt to set an attribute on NULL
>
> Thank you for your help.
>
> Regars,
> B.
>
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-- 
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265

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