Entering edit mode
Jenny Drnevich
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2.2k
@jenny-drnevich-382
Last seen 10.0 years ago
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