ANNOUNCING: BIOCONDUCTOR CHICAGO 2007
This 3-day course (1-3 Oct 2007) on Northwestern University Medical
School's downtown Chicago campus will cover advanced topics in
genomics and
proteomics data analysis. Morning lectures and afternoon lab sessions
will
address a range of topics including microarray data quality
assessment,
Illumina microarray data, gene set enrichment analysis, inference on
graphs
and networks, and RWebServices. Visit the following link for
registration
and more information.
http://daisy.prevmed.northwestern.edu/~denise/BiocChicago2007
*****************************************************
Denise Scholtens, Ph.D.
Assistant Professor, Department of Preventive Medicine
Northwestern University Medical School
dscholtens at northwestern.edu
Dear Users,
I have recently upgraded the bioconductor package to 2.0 from 1.9.
The
affystart function in affycoretools used to work just fine with bioc
1.9
but I get the following errors on 2.0.
>fnames = c("LKM1_051407.CEL","LKM2_051407.CEL")
> expset = affystart(fnames,plot=FALSE,pca=FALSE,express = c("mas5"))
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...done.
45101 ids to be processed
| |
|####################|
Getting probe level data...
Computing p-values
Making P/M/A Calls
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "se.exprs",
for
signature "ExpressionSet"
In addition: Warning messages:
1: The phenoData class is deprecated, use AnnotatedDataFrame (with
ExpressionSet) instead
2: Incompatible phenoData object. Created a new one.
in: read.affybatch(filenames = filenames, phenoData = phenoData)
Execution halted
I tried to look for se.exprs, but couldn't make any headway. Here's
the
output from sessionInfo()
> sessionInfo()
R version 2.5.0 (2007-04-23)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US
.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.
UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8
;LC_IDENTIFICATION=C
attached base packages:
[1] "splines" "tools" "stats" "graphics" "grDevices"
"utils"
[7] "datasets" "methods" "base"
other attached packages:
mouse4302 mouse4302cdf affycoretools annaffy xtable
"1.16.0" "1.16.0" "1.8.0" "1.8.1" "1.4-6"
gcrma matchprobes biomaRt RCurl XML
"2.8.1" "1.8.1" "1.10.0" "0.8-0" "1.7-1"
limma affy affyio GOstats Category
"2.10.5" "1.14.1" "1.4.0" "2.2.6" "2.2.3"
Matrix lattice genefilter survival KEGG
"0.99875-2" "0.15-4" "1.14.1" "2.31" "1.16.1"
RBGL annotate Biobase GO graph
"1.12.0" "1.14.1" "1.14.0" "1.16.0" "1.14.2"
Thanks for the help,
Sachin Mathur
2027 Kansas Life Sciences Innovations Center
3901 Rainbow Blvd.
Kansas City, KS 66160-7401
Phone: (913) 588-5966
Fax: (913) 588-5677
smathur at kumc.edu
Hi Sachin,
Sachin Mathur wrote:
> Dear Users,
>
> I have recently upgraded the bioconductor package to 2.0 from 1.9.
The
> affystart function in affycoretools used to work just fine with bioc
1.9
> but I get the following errors on 2.0.
>
>> fnames = c("LKM1_051407.CEL","LKM2_051407.CEL")
>> expset = affystart(fnames,plot=FALSE,pca=FALSE,express = c("mas5"))
> background correction: mas
> PM/MM correction : mas
> expression values: mas
> background correcting...done.
> 45101 ids to be processed
> | |
> |####################|
> Getting probe level data...
> Computing p-values
> Making P/M/A Calls
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "se.exprs",
for
> signature "ExpressionSet"
> In addition: Warning messages:
> 1: The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead
> 2: Incompatible phenoData object. Created a new one.
> in: read.affybatch(filenames = filenames, phenoData = phenoData)
> Execution halted
>
>
> I tried to look for se.exprs, but couldn't make any headway. Here's
the
> output from sessionInfo()
>
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_
US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U
S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF
-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] "splines" "tools" "stats" "graphics" "grDevices"
> "utils"
> [7] "datasets" "methods" "base"
>
> other attached packages:
> mouse4302 mouse4302cdf affycoretools annaffy
xtable
> "1.16.0" "1.16.0" "1.8.0" "1.8.1"
"1.4-6"
> gcrma matchprobes biomaRt RCurl
XML
> "2.8.1" "1.8.1" "1.10.0" "0.8-0"
"1.7-1"
> limma affy affyio GOstats
Category
> "2.10.5" "1.14.1" "1.4.0" "2.2.6"
"2.2.3"
> Matrix lattice genefilter survival
KEGG
> "0.99875-2" "0.15-4" "1.14.1" "2.31"
"1.16.1"
> RBGL annotate Biobase GO
graph
> "1.12.0" "1.14.1" "1.14.0" "1.16.0"
"1.14.2"
Looks like mismatched versions. Both affy and affycoretools are old. I
would update:
biocLite("Biobase")
library(Biobase)
repos <- biocReposList()
update.packages(repos=repos, ask=FALSE)
Best,
Jim
>
> Thanks for the help,
>
> Sachin Mathur
> 2027 Kansas Life Sciences Innovations Center
> 3901 Rainbow Blvd.
> Kansas City, KS 66160-7401
> Phone: (913) 588-5966
> Fax: (913) 588-5677
> smathur at kumc.edu
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
Dear Jim,
I finally managed to get our IT to sort out the firewall issue and
update the packages as you had indicated, but I still get the same
error.
> expset = affystart(fnames,plot=FALSE,pca=FALSE,express = c("mas5"))
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...done.
31099 ids to be processed
| |
|####################|
Getting probe level data...
Computing p-values
Making P/M/A Calls
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "se.exprs",
for
signature "ExpressionSet"
In addition: Warning messages:
1: The phenoData class is deprecated, use AnnotatedDataFrame (with
ExpressionSet) instead
2: Incompatible phenoData object. Created a new one.
in: read.affybatch(filenames = filenames, phenoData = phenoData)
Execution halted
> sessionInfo()
R version 2.5.0 (2007-04-23)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US
.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.
UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8
;LC_IDENTIFICATION=C
attached base packages:
[1] "splines" "tools" "stats" "graphics" "grDevices"
"utils"
[7] "datasets" "methods" "base"
other attached packages:
rat2302cdf affycoretools annaffy xtable gcrma
"1.16.0" "1.8.0" "1.8.1" "1.4-6" "2.8.1"
matchprobes biomaRt RCurl XML GOstats
"1.8.1" "1.10.1" "0.8-0" "1.7-1" "2.2.6"
Category Matrix lattice genefilter survival
"2.2.3" "0.999375-0" "0.16-2" "1.14.1" "2.32"
KEGG RBGL annotate GO graph
"1.16.1" "1.12.0" "1.14.1" "1.16.0" "1.14.2"
limma affy affyio Biobase
"2.10.5" "1.14.2" "1.4.1" "1.14.1"
While updating the packages, I got some warnings w.r.t. the Matrix
package, but did not get any error messages.
Regards,
Sachin
>>> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> 7/5/2007 4:14 PM
>>>
Hi Sachin,
Sachin Mathur wrote:
> Dear Users,
>
> I have recently upgraded the bioconductor package to 2.0 from 1.9.
The
> affystart function in affycoretools used to work just fine with bioc
1.9
> but I get the following errors on 2.0.
>
>> fnames = c("LKM1_051407.CEL","LKM2_051407.CEL")
>> expset = affystart(fnames,plot=FALSE,pca=FALSE,express = c("mas5"))
> background correction: mas
> PM/MM correction : mas
> expression values: mas
> background correcting...done.
> 45101 ids to be processed
> | |
> |####################|
> Getting probe level data...
> Computing p-values
> Making P/M/A Calls
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "se.exprs",
for
> signature "ExpressionSet"
> In addition: Warning messages:
> 1: The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead
> 2: Incompatible phenoData object. Created a new one.
> in: read.affybatch(filenames = filenames, phenoData = phenoData)
> Execution halted
>
>
> I tried to look for se.exprs, but couldn't make any headway. Here's
the
> output from sessionInfo()
>
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> x86_64-unknown-linux-gnu
>
> locale:
>
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US
.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.
UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8
;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] "splines" "tools" "stats" "graphics" "grDevices"
> "utils"
> [7] "datasets" "methods" "base"
>
> other attached packages:
> mouse4302 mouse4302cdf affycoretools annaffy
xtable
> "1.16.0" "1.16.0" "1.8.0" "1.8.1"
"1.4-6"
> gcrma matchprobes biomaRt RCurl
XML
> "2.8.1" "1.8.1" "1.10.0" "0.8-0"
"1.7-1"
> limma affy affyio GOstats
Category
> "2.10.5" "1.14.1" "1.4.0" "2.2.6"
"2.2.3"
> Matrix lattice genefilter survival
KEGG
> "0.99875-2" "0.15-4" "1.14.1" "2.31"
"1.16.1"
> RBGL annotate Biobase GO
graph
> "1.12.0" "1.14.1" "1.14.0" "1.16.0"
"1.14.2"
Looks like mismatched versions. Both affy and affycoretools are old. I
would update:
biocLite("Biobase")
library(Biobase)
repos <- biocReposList()
update.packages(repos=repos, ask=FALSE)
Best,
Jim
>
> Thanks for the help,
>
> Sachin Mathur
> 2027 Kansas Life Sciences Innovations Center
> 3901 Rainbow Blvd.
> Kansas City, KS 66160-7401
> Phone: (913) 588-5966
> Fax: (913) 588-5677
> smathur at kumc.edu
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
Hi Sachin,
I fixed the problem and pushed to the release repository. The patched
version of affycoretools will be 1.8.1, and should appear in the next
few days.
Thanks for the bug report.
Best,
Jim
Sachin Mathur wrote:
> Dear Jim,
>
> I finally managed to get our IT to sort out the firewall issue and
> update the packages as you had indicated, but I still get the same
> error.
>
>> expset = affystart(fnames,plot=FALSE,pca=FALSE,express = c("mas5"))
> background correction: mas
> PM/MM correction : mas
> expression values: mas
> background correcting...done.
> 31099 ids to be processed
> | |
> |####################|
> Getting probe level data...
> Computing p-values
> Making P/M/A Calls
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "se.exprs",
for
> signature "ExpressionSet"
> In addition: Warning messages:
> 1: The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead
> 2: Incompatible phenoData object. Created a new one.
> in: read.affybatch(filenames = filenames, phenoData = phenoData)
> Execution halted
>
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_
US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U
S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF
-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] "splines" "tools" "stats" "graphics" "grDevices"
> "utils"
> [7] "datasets" "methods" "base"
>
> other attached packages:
> rat2302cdf affycoretools annaffy xtable
gcrma
> "1.16.0" "1.8.0" "1.8.1" "1.4-6"
"2.8.1"
> matchprobes biomaRt RCurl XML
GOstats
> "1.8.1" "1.10.1" "0.8-0" "1.7-1"
"2.2.6"
> Category Matrix lattice genefilter
survival
> "2.2.3" "0.999375-0" "0.16-2" "1.14.1"
"2.32"
> KEGG RBGL annotate GO
graph
> "1.16.1" "1.12.0" "1.14.1" "1.16.0"
"1.14.2"
> limma affy affyio Biobase
> "2.10.5" "1.14.2" "1.4.1" "1.14.1"
>
> While updating the packages, I got some warnings w.r.t. the Matrix
> package, but did not get any error messages.
>
> Regards,
> Sachin
>
>
>>>> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> 7/5/2007 4:14 PM
>>>
> Hi Sachin,
>
> Sachin Mathur wrote:
>> Dear Users,
>>
>> I have recently upgraded the bioconductor package to 2.0 from 1.9.
> The
>> affystart function in affycoretools used to work just fine with
bioc
> 1.9
>> but I get the following errors on 2.0.
>>
>>> fnames = c("LKM1_051407.CEL","LKM2_051407.CEL")
>>> expset = affystart(fnames,plot=FALSE,pca=FALSE,express =
c("mas5"))
>> background correction: mas
>> PM/MM correction : mas
>> expression values: mas
>> background correcting...done.
>> 45101 ids to be processed
>> | |
>> |####################|
>> Getting probe level data...
>> Computing p-values
>> Making P/M/A Calls
>> Error in function (classes, fdef, mtable) :
>> unable to find an inherited method for function "se.exprs",
> for
>> signature "ExpressionSet"
>> In addition: Warning messages:
>> 1: The phenoData class is deprecated, use AnnotatedDataFrame (with
>> ExpressionSet) instead
>> 2: Incompatible phenoData object. Created a new one.
>> in: read.affybatch(filenames = filenames, phenoData = phenoData)
>> Execution halted
>>
>>
>> I tried to look for se.exprs, but couldn't make any headway. Here's
> the
>> output from sessionInfo()
>>
>>> sessionInfo()
>> R version 2.5.0 (2007-04-23)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_
US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U
S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF
-8;LC_IDENTIFICATION=C
>> attached base packages:
>> [1] "splines" "tools" "stats" "graphics" "grDevices"
>> "utils"
>> [7] "datasets" "methods" "base"
>>
>> other attached packages:
>> mouse4302 mouse4302cdf affycoretools annaffy
> xtable
>> "1.16.0" "1.16.0" "1.8.0" "1.8.1"
> "1.4-6"
>> gcrma matchprobes biomaRt RCurl
> XML
>> "2.8.1" "1.8.1" "1.10.0" "0.8-0"
> "1.7-1"
>> limma affy affyio GOstats
> Category
>> "2.10.5" "1.14.1" "1.4.0" "2.2.6"
> "2.2.3"
>> Matrix lattice genefilter survival
> KEGG
>> "0.99875-2" "0.15-4" "1.14.1" "2.31"
> "1.16.1"
>> RBGL annotate Biobase GO
> graph
>> "1.12.0" "1.14.1" "1.14.0" "1.16.0"
> "1.14.2"
>
> Looks like mismatched versions. Both affy and affycoretools are old.
I
>
> would update:
>
> biocLite("Biobase")
> library(Biobase)
> repos <- biocReposList()
> update.packages(repos=repos, ask=FALSE)
>
> Best,
>
> Jim
>
>
>> Thanks for the help,
>>
>> Sachin Mathur
>> 2027 Kansas Life Sciences Innovations Center
>> 3901 Rainbow Blvd.
>> Kansas City, KS 66160-7401
>> Phone: (913) 588-5966
>> Fax: (913) 588-5677
>> smathur at kumc.edu
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
