Hi, all,
When I ran my old chip data (RN U34 chips) with gcrma, I got the
following error. I had no problem with other chip types. Can someone
give me some inputs on this? Thank you.
> gcrma.ob<-gcrma(ob)
Computing affinitiesError in get(x, envir, mode, inherits) : variable
"rnu34probe" was not found
I am using R 2.0.1 and gcrma 1.1.3.
Best,
Puhong
[[alternative HTML version deleted]]
Please check the probepackage name and cdfpackage name for your chip
type
first.
The ones provided on bioconductor usually have names like
"CHIPcdf" and "CHIPprobe" where CHIP is the chip type such as
"hgu133a".
If your probe package is created with a name following different
convention, gcrma may not recognize it.
On Tue, 10 May 2005, Puhong Gao wrote:
> Hi, all,
>
> When I ran my old chip data (RN U34 chips) with gcrma, I got the
following error. I had no problem with other chip types. Can someone
give me some inputs on this? Thank you.
>
> > gcrma.ob<-gcrma(ob)
> Computing affinitiesError in get(x, envir, mode, inherits) :
variable "rnu34probe" was not found
>
> I am using R 2.0.1 and gcrma 1.1.3.
>
> Best,
>
> Puhong
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
Puhong Gao wrote:
> Hi, all,
>
> When I ran my old chip data (RN U34 chips) with gcrma, I got the
following error. I had no problem with other chip types. Can someone
give me some inputs on this? Thank you.
>
>
>>gcrma.ob<-gcrma(ob)
>
> Computing affinitiesError in get(x, envir, mode, inherits) :
variable "rnu34probe" was not found
With the version of gcrma you are using, you should not be able to get
to that point without automagically installing the correct probe
package. How about trying
library(reposTools)
install.packages2("rnu34probe")
and then run gcrma() again.
Best,
Jim
>
> I am using R 2.0.1 and gcrma 1.1.3.
>
> Best,
>
> Puhong
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
Hi, Zhijin and Jim,
Thank you both for your quick input.
Indeed, R automatically initiated the installation of "rnu34cdf" and
"rnu34probe" when I first ran GCRMA. Since I got the posted error, I
manually installed rnu34 packages downloaded from Bioconductor site
and got
the same error when GCRMA was run. I did check the package names and
found
no problem. By the way, I ran GCRMA on rgu34a chip data without
problem
yesterday. Is there anything else I should check? Thank you.
Best,
Puhong
----- Original Message -----
From: "Zhijin Wu" <zwu@jhsph.edu>
To: "Puhong Gao" <pgao@hunter.cuny.edu>
Cc: <bioconductor@stat.math.ethz.ch>
Sent: Tuesday, May 10, 2005 3:00 PM
Subject: Re: [BioC] GCRMA error
> Please check the probepackage name and cdfpackage name for your chip
type
> first.
> The ones provided on bioconductor usually have names like
> "CHIPcdf" and "CHIPprobe" where CHIP is the chip type such as
"hgu133a".
> If your probe package is created with a name following different
> convention, gcrma may not recognize it.
>
>
> On Tue, 10 May 2005, Puhong Gao wrote:
>
>> Hi, all,
>>
>> When I ran my old chip data (RN U34 chips) with gcrma, I got the
>> following error. I had no problem with other chip types. Can
someone give
>> me some inputs on this? Thank you.
>>
>> > gcrma.ob<-gcrma(ob)
>> Computing affinitiesError in get(x, envir, mode, inherits) :
variable
>> "rnu34probe" was not found
>>
>> I am using R 2.0.1 and gcrma 1.1.3.
>>
>> Best,
>>
>> Puhong
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
Do you see "rnu34probe" when you do
search()
If yes, what do you get if you do
P <-get("rnu34probe")
On Tue, 10 May 2005, Puhong Gao wrote:
> Hi, Zhijin and Jim,
>
> Thank you both for your quick input.
>
> Indeed, R automatically initiated the installation of "rnu34cdf" and
> "rnu34probe" when I first ran GCRMA. Since I got the posted error, I
> manually installed rnu34 packages downloaded from Bioconductor site
and got
> the same error when GCRMA was run. I did check the package names and
found
> no problem. By the way, I ran GCRMA on rgu34a chip data without
problem
> yesterday. Is there anything else I should check? Thank you.
>
> Best,
>
> Puhong
>
> ----- Original Message -----
> From: "Zhijin Wu" <zwu@jhsph.edu>
> To: "Puhong Gao" <pgao@hunter.cuny.edu>
> Cc: <bioconductor@stat.math.ethz.ch>
> Sent: Tuesday, May 10, 2005 3:00 PM
> Subject: Re: [BioC] GCRMA error
>
>
> > Please check the probepackage name and cdfpackage name for your
chip type
> > first.
> > The ones provided on bioconductor usually have names like
> > "CHIPcdf" and "CHIPprobe" where CHIP is the chip type such as
"hgu133a".
> > If your probe package is created with a name following different
> > convention, gcrma may not recognize it.
> >
> >
> > On Tue, 10 May 2005, Puhong Gao wrote:
> >
> >> Hi, all,
> >>
> >> When I ran my old chip data (RN U34 chips) with gcrma, I got the
> >> following error. I had no problem with other chip types. Can
someone give
> >> me some inputs on this? Thank you.
> >>
> >> > gcrma.ob<-gcrma(ob)
> >> Computing affinitiesError in get(x, envir, mode, inherits) :
variable
> >> "rnu34probe" was not found
> >>
> >> I am using R 2.0.1 and gcrma 1.1.3.
> >>
> >> Best,
> >>
> >> Puhong
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>
>
Hi, Zhijin,
I don't see "rnu34probe" and other chip packages (see below)
> search()
[1] ".GlobalEnv" "package:splines" "package:gcrma"
[4] "package:matchprobes" "package:affy" "package:reposTools"
[7] "package:Biobase" "package:tools" "package:methods"
[10] "package:stats" "package:graphics" "package:grDevices"
[13] "package:utils" "package:datasets" "Autoloads"
[16] "package:base"
>
I just tried GCRMA on RG U34a data and it worked without a problem
(see
below). (R was started in a different folder, if it means anything.).
So, it
should be rnu34 chip specific.
> local({pkg <- select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
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
Loading required package: matchprobes
> search()
[1] ".GlobalEnv" "package:gcrma" "package:matchprobes"
[4] "package:affy" "package:reposTools" "package:Biobase"
[7] "package:tools" "package:methods" "package:stats"
[10] "package:graphics" "package:grDevices" "package:utils"
[13] "package:datasets" "Autoloads" "package:base"
> g.so<-gcrma(so)
Computing affinities.Done.
Adjusting for optical effect..............................Done.
Adjusting for non-specific binding..............................Done.
Normalizing
Calculating Expression
>
Best,
Puhong
----- Original Message -----
From: "Zhijin Wu" <zwu@jhsph.edu>
To: "Puhong Gao" <pgao@hunter.cuny.edu>
Cc: <bioconductor@stat.math.ethz.ch>
Sent: Tuesday, May 10, 2005 5:15 PM
Subject: Re: [BioC] GCRMA error
> Do you see "rnu34probe" when you do
>
> search()
>
> If yes, what do you get if you do
>
> P <-get("rnu34probe")
>
Puhong Gao wrote:
> Hi, Zhijin,
>
> I don't see "rnu34probe" and other chip packages (see below)
>
>> search()
>
> [1] ".GlobalEnv" "package:splines" "package:gcrma"
> [4] "package:matchprobes" "package:affy" "package:reposTools"
> [7] "package:Biobase" "package:tools" "package:methods"
> [10] "package:stats" "package:graphics" "package:grDevices"
> [13] "package:utils" "package:datasets" "Autoloads"
> [16] "package:base"
The existing rnu34probe package on BioC is broken due to a difference
in
how things were built when it was originally made, and how things are
currently built. I have sent a corrected package to Puhong privately
and
will be sending the same to Seth for posting on the website.
Best,
Jim
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623