[BioC] past bioc releases

[Martin Morgan]

"wangchuanming" <wangchuanming at 126.com> writes:

> Dear Simon,
>
> Thank you very much for your help!
>
> Now I solved the problem following your advice. After I loaded "genefilter",the function "rowSds" run. At last I got the results.But there are some other little problems and I wonder why they happened.
>
> 1/
>> sum.sam.out<-summary(sam.out,30,ll=FALSE);
> Error in .local(object, ...) : unused arguments in argument((ll = FALSE)) 
>
> The error message above appears in R 2.9 but not in R 2.4

your 'sam.out' instance is a class of object "SAM". To see this, try

  > class(sam.out)

To see what functions are available on this object, try

  > ?"SAM-class"

and

  > help.sam(summary)

In this particular case, I believe that 'll' refered to LocusLink
information, and this is not so useful these days; since you were
invoking summary with ll=FALSE, there would seem to be little harm in
just omitting it.

> 2/
>> library(estrogen);
> Error in library(estrogen) : Packages not available:'estrogen'
>
> The error message above appears in all version of R. "estrogen" is
> the package found in my reference book. This step is optional,so I
> slip it.

Bioconductor has a number of 'experimental data' packages
available. Likely elsewhere in your book there is the command (or one
that accomplishes the same thing)

  source('http://bioconductor.org/biocLite.R')
  biocLite('estrogen')

this installs the 'estrogen' package, so that it is available in
subsequent sessions. You will then be able to evaluate

  library('estrogen')

in any session where  you want to access this data.

> 3/
>> heatmap(exprs(AffyExpData)[sel,],col=gentlecol(256));
> Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + :function not available:"gentlecol"
>
>
> The error message above appears in all version of R. "gentlecol" is
> also the function found in my reference book. I replace it by below:
>
>> heatmap(exprs(AffyExpData)[sel,],col =rainbow(256)); 
> or
>> heatmap(exprs(AffyExpData)[sel,],col = cm.colors(256)); 
>
> It runs. But I wonder that is there many errors in my book?  Whether
> 'estrogen' and "gentlecol" are very old and have been removed now or
> did not exist at all?

gentlecol is defined in the estrogen package, so it should be
available once you have estrogen loaded.

Martin

>
> Yours hopefully,
>
>
> 2009-05-17 
>
>
>
> wangchuanming 
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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