[BioC] problems with Affy vignette and affybatch objects

[Jenny Drnevich]

Hi,

There's some problem with the default value for affybatch objects (if this 
is the correct description) that's appeared in affy 1.12.0, which also can 
be seen in the affy vignette. Previously, when I typed in the name of an 
affybatch object at the command line, I'd get the same output as if I had 
put 'show(abatch)':

 > raw
AffyBatch object
size of arrays=602x602 features (53806 kb)
cdf=RAE230A (15923 affyids)
number of samples=19
number of genes=15923
annotation=rae230a

 > show(raw)
AffyBatch object
size of arrays=602x602 features (53806 kb)
cdf=RAE230A (15923 affyids)
number of samples=19
number of genes=15923
annotation=rae230a

 > sessionInfo()
Version 2.3.1 Patched (2006-08-06 r38829)
i386-pc-mingw32

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
    rae230acdf  affyQCReport    simpleaffy    reposTools         made4
      "1.12.0"      "1.10.0"       "2.6.0"      "1.10.0"       "1.6.0"
scatterplot3d          ade4       affyPLM         gcrma   matchprobes
      "0.3-24"       "1.4-1"       "1.8.0"       "2.4.1"       "1.4.0"
      affydata affycoretools       GOstats      Category      hgu95av2
       "1.8.0"       "1.4.0"       "1.6.0"       "1.4.1"      "1.12.0"
          KEGG      multtest    genefilter      survival        xtable
      "1.12.0"      "1.10.2"      "1.10.1"        "2.26"       "1.3-2"
          RBGL      annotate            GO         graph         Ruuid
       "1.8.1"      "1.10.0"      "1.12.0"      "1.10.6"      "1.10.0"
         limma          affy        affyio       Biobase       RWinEdt
       "2.7.9"      "1.10.0"       "1.0.0"      "1.10.1"       "1.7-4"

However, now when I just type in the name of the affybatch object, the 
entire contents of the affybatch object is output! (current sessionInfo 
below). This is also in the vignette (October 3, 2006), on page 11-251 (did 
no one notice the vignette was 271 pages long?!?). I had noticed that the 
previous vignette from affy 1.10.0 (April 25, 2006) was also 271 pages long 
when called from my installation, but at the time when I went back and 
checked on the Bioconductor website, the vignette listed there was the 
right length. I thought the problem had been corrected, and since I wasn't 
having any trouble typing in the name of the affybatch object to get the 
summary, I didn't report it.

One last thing - were there no changes to affy for the Bioconductor 1.9 
release? The beginning of the vignette (Oct 3, 2006) still has listed 
'Changes for affy in BioC 1.8 release' in section 2, along with all the 
same information as in the previous vignette.

Thanks,
Jenny

 >raw
#many, many, many lines deleted...
a18   15     4   1
a19   15     4   2
a20   15     5   1
a21   15     5   2
Slot "varLabels":
Slot "varLabels":$Week
[1] "Week"

Slot "varLabels":$Group
[1] "Group"

Slot "varLabels":$Rep
[1] "Replicate"

Slot "varMetadata":
NULL data frame with 0 rows

 > show(raw)
AffyBatch object
size of arrays=602x602 features (53806 kb)
cdf=RAE230A (15923 affyids)
number of samples=19
number of genes=15923
annotation=rae230a

 > sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
    rae230acdf  affyQCReport    simpleaffy         made4 scatterplot3d
      "1.14.0"      "1.12.0"       "2.8.0"       "1.8.0"      "0.3-24"
          ade4       affyPLM         gcrma   matchprobes      affydata
       "1.4-2"      "1.10.0"       "2.6.0"       "1.6.0"      "1.10.0"
affycoretools       biomaRt         RCurl           XML       GOstats
       "1.6.0"       "1.8.0"       "0.7-0"     "0.99-93"       "2.0.0"
      Category    genefilter      survival          KEGG          RBGL
       "2.0.0"      "1.12.0"        "2.29"      "1.14.0"      "1.10.0"
      annotate            GO         graph         limma          affy
      "1.12.0"      "1.14.0"      "1.12.0"       "2.9.1"      "1.12.0"
        affyio       Biobase       RWinEdt
       "1.2.0"      "1.12.0"       "1.7-5"
 >



Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu