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Hilmar Lapp
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@hilmar-lapp-1299
Last seen 10.2 years ago
Hi,
aside from Affy's commercial arrays we also use custom arrays, for
which we built the cdf and probe packages in order to be able to
analyze them with Bioconductor.
So far the custom arrays and their packages have worked fine, e.g.
using gcRMA (just.gcrma()). However, they result in an error with
SimpleAffy (which works fine with Affy's commercial arrays). The error
message seems to indicate that the respective cdf and probe packages
aren't present ("I'm sorry I do not know about chip type:
gngnf1musacdf"), but as a matter of fact they are. Issuing
> library(gngnf1musacdf)
before the qc() call has no effect (i.e., it itself succeeds, but
doesn't help qc() succeed).
Below is a pertinent transcript. R is v2.0.1 and simpleaffy is v1.3.2.
Does anyone have any idea what's going on or how to track down the
root
cause, and possibly even how to fix the problem?
-hilmar
> library(simpleaffy)
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
Loading required package: reposTools
Welcome to 'simpleaffy'
Produced by The Paterson Institute for Cancer Research
and funded by CANCER RESEARCH UK.
http://bioinformatics.picr.man.ac.uk/simpleaffy
mailto: microarray at picr.man.ac.uk
Attaching package 'simpleaffy':
The following object(s) are masked from package:datasets :
volcano
> x <- read.affy("covdesc.txt")
> x.mas5 <- call.exprs(x,"mas5")
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls...
......done.
scaling to a TGT of 100 ...Scale factor for: MGGH05051305.CEL
1.29763874700679
Scale factor for: MGGH05051306.CEL 1.36310544263026
Scale factor for: MGGH05051307.CEL 2.37128019446524
Scale factor for: MGGH05051308.CEL 2.81635815428688
Scale factor for: MGGH05051309.CEL 1.22141352555512
Scale factor for: MGGH05051310.CEL 1.12787439983082
> qc <- qc(x,x.mas5)
Error in qc.affy(unnormalised, ...) : I'm sorry I do not know about
chip
type: gngnf1musacdf
> installed.packages()
Package LibPath
Version
Priority Bundle
affy "affy" "C:/PROGRA~1/R/rw2001/library"
"1.5.8"
NA NA
base "base" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
Biobase "Biobase" "C:/PROGRA~1/R/rw2001/library"
"1.5.0"
NA NA
boot "boot" "C:/PROGRA~1/R/rw2001/library"
"1.2-20" "recommended" NA
class "class" "C:/PROGRA~1/R/rw2001/library"
"7.2-10" "recommended" "VR"
cluster "cluster" "C:/PROGRA~1/R/rw2001/library"
"1.9.6"
"recommended" NA
datasets "datasets" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
foreign "foreign" "C:/PROGRA~1/R/rw2001/library"
"0.8-0"
"recommended" NA
gcrma "gcrma" "C:/PROGRA~1/R/rw2001/library"
"1.1.3"
NA NA
gngnf1bacdf "gngnf1bacdf" "C:/PROGRA~1/R/rw2001/library"
"1.4.8"
NA NA
gngnf1baprobe "gngnf1baprobe" "C:/PROGRA~1/R/rw2001/library"
"0.0.1"
NA NA
gngnf1musacdf "gngnf1musacdf" "C:/PROGRA~1/R/rw2001/library"
"1.4.8"
NA NA
gngnf1musaprobe "gngnf1musaprobe" "C:/PROGRA~1/R/rw2001/library"
"0.0.1"
NA NA
graphics "graphics" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
grDevices "grDevices" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
grid "grid" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
hgu133acdf "hgu133acdf" "C:/PROGRA~1/R/rw2001/library"
"1.4.3"
NA NA
hgu133aprobe "hgu133aprobe" "C:/PROGRA~1/R/rw2001/library" "1.0"
NA NA
hgu95acdf "hgu95acdf" "C:/PROGRA~1/R/rw2001/library"
"1.4.1"
NA NA
hgu95aprobe "hgu95aprobe" "C:/PROGRA~1/R/rw2001/library" "1.0"
NA NA
hgu95av2cdf "hgu95av2cdf" "C:/PROGRA~1/R/rw2001/library"
"1.4.3"
NA NA
hgu95av2probe "hgu95av2probe" "C:/PROGRA~1/R/rw2001/library" "1.0"
NA NA
KernSmooth "KernSmooth" "C:/PROGRA~1/R/rw2001/library"
"2.22-14" "recommended" NA
lattice "lattice" "C:/PROGRA~1/R/rw2001/library"
"0.10-14" "recommended" NA
MASS "MASS" "C:/PROGRA~1/R/rw2001/library"
"7.2-10" "recommended" "VR"
matchprobes "matchprobes" "C:/PROGRA~1/R/rw2001/library"
"1.0.12" NA NA
methods "methods" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
mgcv "mgcv" "C:/PROGRA~1/R/rw2001/library"
"1.1-8"
"recommended" NA
mgu74av2cdf "mgu74av2cdf" "C:/PROGRA~1/R/rw2001/library"
"1.4.3"
NA NA
mgu74av2probe "mgu74av2probe" "C:/PROGRA~1/R/rw2001/library" "1.0"
NA NA
nlme "nlme" "C:/PROGRA~1/R/rw2001/library"
"3.1-53" "recommended" NA
nnet "nnet" "C:/PROGRA~1/R/rw2001/library"
"7.2-10" "recommended" "VR"
rae230acdf "rae230acdf" "C:/PROGRA~1/R/rw2001/library"
"1.4.3"
NA NA
rae230aprobe "rae230aprobe" "C:/PROGRA~1/R/rw2001/library" "1.0"
NA NA
reposTools "reposTools" "C:/PROGRA~1/R/rw2001/library"
"1.5.3"
NA NA
rgu34acdf "rgu34acdf" "C:/PROGRA~1/R/rw2001/library"
"1.4.3"
NA NA
rgu34aprobe "rgu34aprobe" "C:/PROGRA~1/R/rw2001/library" "1.0"
NA NA
rpart "rpart" "C:/PROGRA~1/R/rw2001/library"
"3.1-20" "recommended" NA
simpleaffy "simpleaffy" "C:/PROGRA~1/R/rw2001/library"
"1.3.2"
NA NA
spatial "spatial" "C:/PROGRA~1/R/rw2001/library"
"7.2-10" "recommended" "VR"
splines "splines" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
stats "stats" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
stats4 "stats4" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
survival "survival" "C:/PROGRA~1/R/rw2001/library"
"2.15"
"recommended" NA
tcltk "tcltk" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
tools "tools" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
utils "utils" "C:/PROGRA~1/R/rw2001/library"
"2.0.1"
"base" NA
Depends
Suggests
affy "R (>= 1.9.0), Biobase (>= 1.4.22), reposTools"
"tkWidgets (>= 1.2.2), affydata"
base NA NA
Biobase "R (>= 1.9.0),tools"
"widgetTools, tkWidgets"
boot "R (>= 2.0.0), graphics, stats"
"survival"
class "R (>= 2.0.0), graphics, stats"
"lattice, nlme, survival"
cluster "R (>= 1.9), stats, graphics, utils" NA
datasets NA NA
foreign "R (>= 2.0.0)" NA
gcrma "R (>= 1.9), affy (>= 1.4), matchprobes"
"affydata"
gngnf1bacdf NA NA
gngnf1baprobe "R (>= 1.6), matchprobes (>= 1.0.12)" NA
gngnf1musacdf NA NA
gngnf1musaprobe "R (>= 1.6), matchprobes (>= 1.0.12)" NA
graphics "grDevices" NA
grDevices NA NA
grid "grDevices"
"lattice"
hgu133acdf NA NA
hgu133aprobe "R (>= 1.6), matchprobes" NA
hgu95acdf NA NA
hgu95aprobe "R (>= 1.6), matchprobes" NA
hgu95av2cdf NA NA
hgu95av2probe "R (>= 1.6), matchprobes" NA
KernSmooth "R (>= 1.9.0)" "MASS"
lattice "R (>= 2.0.0)" "grid"
MASS "R (>= 2.0.0), graphics, stats"
"lattice, nlme, survival"
matchprobes "R (>= 1.8.0), Biobase (>= 1.4.1)"
"hgu95av2cdf, hgu95av2probe, hu6800cdf, hu6800probe"
methods NA NA
mgcv "R (>= 1.9.0)" "nlme
(>= 3.1-52), MASS (>= 7.2-2)"
mgu74av2cdf NA NA
mgu74av2probe "R (>= 1.6), matchprobes" NA
nlme "graphics, stats, R(>= 2.0.0)" NA
nnet "R (>= 2.0.0), graphics, stats"
"lattice, nlme, survival"
rae230acdf NA NA
rae230aprobe "R (>= 1.6), matchprobes (>= 1.0.8)" NA
reposTools "R (>= 1.8.0), tools" "XML"
rgu34acdf NA NA
rgu34aprobe "R (>= 1.6), matchprobes" NA
rpart "R (>= 2.0.0)"
"survival"
simpleaffy "R (>= 1.9.0), affy" NA
spatial "R (>= 2.0.0), graphics, stats"
"lattice, nlme, survival"
splines NA NA
stats NA NA
stats4 "graphics, stats, methods" NA
survival "stats, utils, graphics, splines, R (>= 2.0.0)" NA
tcltk NA NA
tools NA NA
utils NA NA
>
--
-------------------------------------------------------------
Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
