Dear all,
Could it be that function mas5calls() no longer returns the p-values,
since se.exprs does no longer exist?
I get:
pr.call <- mas5calls(pr)
call <-exprs(pr.call)
pval <-se.exprs(pr.call) ||
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "se.exprs", for
signature "ExpressionSet"
Interestingly, the source code in "mas5.R" still creates an
ExpressionSet with "se.exprs=p".
sessionInfo()
R version 2.5.0 (2007-04-23)
i386-apple-darwin8.9.1
locale:
C
attached base packages:
[1] "tools" "stats" "graphics" "grDevices" "utils" "datasets"
[7] "methods" "base"
other attached packages:
hgu95av2cdf affy affyio Biobase
"1.16.0" "1.14.0" "1.4.0" "1.14.0"
Best regards
Christian
[Bioc-devel] pval in mas5calls()
4 messages · cstrato, Martin Morgan, Seth Falcon
Christian: The values are there, just not accessible with se.exprs. Try 'assayData(obj)[["se.exprs"]]':
example(mas5calls)
ms5cll> data(affybatch.example) ms5cll> PACalls <- mas5calls(affybatch.example) Getting probe level data... Computing p-values Making P/M/A Calls
dim(assayData(PACalls)[["se.exprs"]])
[1] 150 3 Martin cstrato <cstrato at aon.at> writes:
Dear all,
Could it be that function mas5calls() no longer returns the p-values,
since se.exprs does no longer exist?
I get:
pr.call <- mas5calls(pr)
call <-exprs(pr.call)
pval <-se.exprs(pr.call) ||
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "se.exprs", for
signature "ExpressionSet"
Interestingly, the source code in "mas5.R" still creates an
ExpressionSet with "se.exprs=p".
sessionInfo()
R version 2.5.0 (2007-04-23)
i386-apple-darwin8.9.1
locale:
C
attached base packages:
[1] "tools" "stats" "graphics" "grDevices" "utils" "datasets"
[7] "methods" "base"
other attached packages:
hgu95av2cdf affy affyio Biobase
"1.16.0" "1.14.0" "1.4.0" "1.14.0"
Best regards
Christian
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Martin Morgan Bioconductor / Computational Biology http://bioconductor.org
Dear Martin Thank you for your immediate reply, it works great. (Maybe this could be mentioned in the help file for ?mas5calls) Best regards Christian
Martin Morgan wrote:
Christian: The values are there, just not accessible with se.exprs. Try 'assayData(obj)[["se.exprs"]]':
example(mas5calls)
ms5cll> data(affybatch.example) ms5cll> PACalls <- mas5calls(affybatch.example) Getting probe level data... Computing p-values Making P/M/A Calls
dim(assayData(PACalls)[["se.exprs"]])
[1] 150 3 Martin cstrato <cstrato at aon.at> writes:
Dear all,
Could it be that function mas5calls() no longer returns the p-values,
since se.exprs does no longer exist?
I get:
pr.call <- mas5calls(pr)
call <-exprs(pr.call)
pval <-se.exprs(pr.call) ||
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "se.exprs", for
signature "ExpressionSet"
Interestingly, the source code in "mas5.R" still creates an
ExpressionSet with "se.exprs=p".
sessionInfo()
R version 2.5.0 (2007-04-23)
i386-apple-darwin8.9.1
locale:
C
attached base packages:
[1] "tools" "stats" "graphics" "grDevices" "utils" "datasets"
[7] "methods" "base"
other attached packages:
hgu95av2cdf affy affyio Biobase
"1.16.0" "1.14.0" "1.4.0" "1.14.0"
Best regards
Christian
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
cstrato <cstrato at aon.at> writes:
Dear Martin Thank you for your immediate reply, it works great. (Maybe this could be mentioned in the help file for ?mas5calls)
That's a good idea for the released version. For devel, I wonder if at least the affy package should provide an se.exprs method for ExpressionSets that returns a readable error message if assayData(obj)[["se.exprs"]] does not exits... + seth
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org