[BioC] simpleAffy, custom chip error

Hilmar Lapp hlapp at gnf.org
Tue Jun 21 02:10:32 CEST 2005


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?


> 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.
       mailto: microarray at picr.man.ac.uk

Attaching package 'simpleaffy':

         The following object(s) are masked from package:datasets :


> x <- read.affy("covdesc.txt")
> x.mas5 <- call.exprs(x,"mas5")
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls...
scaling to a TGT of 100 ...Scale factor for: MGGH05051305.CEL
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"
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"
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"
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)"
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

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