[BioC] Unable to get the Platform Table using fData on eset object

[Wolfgang Huber]

Dear Sailu

you need to provide the output of "sessionInfo()" as well as the error 
message you get, or what eaxctly in the result that you get you think is 
wrong. What do you mean by "coming in table format"? Neither "coming" 
nor "table format" are well-defined concepts in the R language.

When I just ran your code chunk, I got:
 > str(platform)
'data.frame':	45101 obs. of  17 variables:
  $ Composite.Element.Name                              : Factor w/ 
45101 levels "Affymetrix:CompositeSequence:Mouse430_2:1415670_at",..: 
45038 45039 45040 45041 45042 45043 45044 45045 45046 45047 ...
  $ Comment.AECompositeName.                            : Factor w/ 
45101 levels "1415670_at","1415671_at",..: 45038 45039 45040 45041 45042 
45043 45044 45045 45046 45047 ...
  $
....[11 more elements] ....


which seems alright to me.

I also got,

 > eset=procset(data, cn[2])
Read 49 items
Warning message:
In eval(expr, envir, enclos) : Cannot attach phenoData

 > sessionInfo()
R version 2.12.0 Under development (unstable) (2010-05-10 r51966)
x86_64-unknown-linux-gnu

locale:
  [1] LC_CTYPE=C             LC_NUMERIC=C           LC_TIME=C
  [4] LC_COLLATE=C           LC_MONETARY=C          LC_MESSAGES=la_AU.utf8
  [7] LC_PAPER=C             LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C       LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] ArrayExpress_1.9.0 Biobase_2.9.0      fortunes_1.3-7

loaded via a namespace (and not attached):
[1] XML_3.1-0             affy_1.27.1           affyio_1.17.0
[4] limma_3.5.3           preprocessCore_1.11.0

Best wishes
	Wolfgang




On 10/05/10 22:25, Sailu Yellaboina wrote:
> Hi
>   I am unable to get the plotform table  using fData on eset object
> downloaded from ArrayExpress.
>
> Here is the example R code.
>
> library(ArrayExpress)
> dataset.name="E-TABM-493"
> data=try(getAE(dataset.name, type="processed"))
> cn=getcolproc(data)
> eset=procset(data, cn[2])
> platform=fData(eset)
>
> The platform is not coming in table format.
>
> Thank You
> Sailu Yellaboina
> Visiting Fellow
> NIEHS, NIH
>
> 	[[alternative HTML version deleted]]
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber