VSN error : 'ny' does not seem to be resulting from vsn
1
0
Entering edit mode
SAURIN ★ 1.1k
@saurin-799
Last seen 7.1 years ago
Hi, I am using R-2.0 with develOK=TRUE. Here, esetSub2 is my differentially expressed gene expression set. >esetSub2X <- getIntensityMatrix(esetSub2); >esetSub2Norm <- vsn(esetSub2,describe.preprocessing = FALSE); vsn: 762 x 6 matrix (1 stratum). Please wait for 10 dots: .......... > esetSub2Train <- esetSub2Norm[,4:6]; Error in validObject(.Object) : Invalid "phenoData" object: FALSE > traceback(); 7: stop(paste("Invalid \"", Class, "\" object: ", errors, sep = "")) 6: validObject(.Object) 5: initialize(value, ...) 4: initialize(value, ...) 3: new("phenoData", pData = pD, varLabels = vL) 2: phenoData(x)[j, , ..., drop = FALSE] 1: esetSub2Norm[, 4:6] > vsnPlotPar(esetSub2Norm, "factors") Error in vsnPlotPar(esetSub2Norm, "factors") : 'ny' does not seem to be resulting from vsn. > vsnPlotPar(esetSub2Norm, "offsets") Error in vsnPlotPar(esetSub2Norm, "offsets") : 'ny' does not seem to be resulting from vsn. > traceback(); 2: stop("'ny' does not seem to be resulting from vsn.") 1: vsnPlotPar(esetSub2Norm, "offsets") is something wrong in my expression set? thank you, Saurin
vsn vsn • 508 views
ADD COMMENT
0
Entering edit mode
@wolfgang-huber-3550
Last seen 3 days ago
EMBL European Molecular Biology Laborat…
Hi Saurin, I answer your questions in reverse order: the error message in vsnPlotPar results from using the option 'describe.preprocessing=FALSE' in the call to vsn. If you use that option, the fitted parameters are not stored in the resulting exprSet, hence there is nothing to plot for vsnPlotPar. Second, what happens if you do esetSub2[,4:6]? And what happens if you call vsn with describe.preprocessing=TRUE (i.e. the default)? If the problem persists, please make the exprSet available so I can have a look. Bw Wolfgang <quote who="Saurin Jani"> > Hi, > > I am using R-2.0 with develOK=TRUE. Here, esetSub2 is > my differentially expressed gene expression set. > >>esetSub2X <- getIntensityMatrix(esetSub2); > >>esetSub2Norm <- vsn(esetSub2,describe.preprocessing = > > FALSE); > vsn: 762 x 6 matrix (1 stratum). Please wait for 10 > dots: .......... > >> esetSub2Train <- esetSub2Norm[,4:6]; > Error in validObject(.Object) : Invalid "phenoData" > object: FALSE > >> traceback(); > 7: stop(paste("Invalid \"", Class, "\" object: ", > errors, sep = "")) > 6: validObject(.Object) > 5: initialize(value, ...) > 4: initialize(value, ...) > 3: new("phenoData", pData = pD, varLabels = vL) > 2: phenoData(x)[j, , ..., drop = FALSE] > 1: esetSub2Norm[, 4:6] > >> vsnPlotPar(esetSub2Norm, "factors") > Error in vsnPlotPar(esetSub2Norm, "factors") : > 'ny' does not seem to be resulting from vsn. > >> vsnPlotPar(esetSub2Norm, "offsets") > Error in vsnPlotPar(esetSub2Norm, "offsets") : > 'ny' does not seem to be resulting from vsn. > >> traceback(); > 2: stop("'ny' does not seem to be resulting from > vsn.") > 1: vsnPlotPar(esetSub2Norm, "offsets") > > > is something wrong in my expression set? > > thank you, > Saurin > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Http: www.dkfz.de/abt0840/whuber ------------------------------------- ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Http: www.dkfz.de/abt0840/whuber
ADD COMMENT
0
Entering edit mode
Hi Dr. Huber, I have done as kept vsn with default TRUE value but I come up with same error for esetSubNorm[,4:6] I have 6 CEL files and I am reading through Readaffy().I am comparing Knock Out (KO) and Wild Type(WT) samples from Mouse embryo Fibroblast Affy data. I have below described expression set, please let me know if you need more values or informatoin for expression set. > library(vsn); > library(stam); > esetSub2Norm <- vsn(esetSub2); vsn: 762 x 6 matrix (1 stratum). Please wait for 10 dots: .......... > vsnPlotPar(esetSub2Norm, "offsets") Here, vsnPlotPar works nice. But > esetSub2Train <- esetSub2Norm[,4:6]; Error in validObject(.Object) : Invalid "phenoData" object: FALSE > phenoData(esetSub2); phenoData object with 3 variables and 6 cases varLabels sample: arbitrary numbering > pData(esetSub2); sample scanner1 scanner2 Fib1C-KO1 1 0 KO Fib1C-KO2 2 0 KO Fib1C-KO3 3 0 KO Fib1C-WT1 4 1 WT Fib1C-WT2 5 1 WT Fib1C-WT3 6 1 WT > exprs(esetSub2) Fib1C-KO1 Fib1C-KO2 Fib1C-KO3 Fib1C-WT1 Fib1C-WT2 Fib1C-WT3 1415768_a_at 8.240705 8.332744 8.176031 8.949155 8.913745 8.858628 1415810_at 7.305646 7.565421 7.219027 6.027602 6.098046 5.857212 1415811_at 6.671428 6.625956 6.554472 5.264805 5.554093 5.674547 and so on.... Thank you, Saurin --- Wolfgang Huber <huber@ebi.ac.uk> wrote: > Hi Saurin, > > I answer your questions in reverse order: the error > message in vsnPlotPar > results from using the option > 'describe.preprocessing=FALSE' in the call > to vsn. If you use that option, the fitted > parameters are not stored in > the resulting exprSet, hence there is nothing to > plot for vsnPlotPar. > > Second, what happens if you do esetSub2[,4:6]? > And what happens if you call vsn with > describe.preprocessing=TRUE (i.e. > the default)? > > If the problem persists, please make the exprSet > available so I can have a > look. > > Bw > Wolfgang > > <quote who="Saurin Jani"> > > Hi, > > > > I am using R-2.0 with develOK=TRUE. Here, esetSub2 > is > > my differentially expressed gene expression set. > > > >>esetSub2X <- getIntensityMatrix(esetSub2); > > > >>esetSub2Norm <- > vsn(esetSub2,describe.preprocessing = > > > > FALSE); > > vsn: 762 x 6 matrix (1 stratum). Please wait for > 10 > > dots: .......... > > > >> esetSub2Train <- esetSub2Norm[,4:6]; > > Error in validObject(.Object) : Invalid > "phenoData" > > object: FALSE > > > >> traceback(); > > 7: stop(paste("Invalid \"", Class, "\" object: ", > > errors, sep = "")) > > 6: validObject(.Object) > > 5: initialize(value, ...) > > 4: initialize(value, ...) > > 3: new("phenoData", pData = pD, varLabels = vL) > > 2: phenoData(x)[j, , ..., drop = FALSE] > > 1: esetSub2Norm[, 4:6] > > > >> vsnPlotPar(esetSub2Norm, "factors") > > Error in vsnPlotPar(esetSub2Norm, "factors") : > > 'ny' does not seem to be resulting from > vsn. > > > >> vsnPlotPar(esetSub2Norm, "offsets") > > Error in vsnPlotPar(esetSub2Norm, "offsets") : > > 'ny' does not seem to be resulting from > vsn. > > > >> traceback(); > > 2: stop("'ny' does not seem to be resulting from > > vsn.") > > 1: vsnPlotPar(esetSub2Norm, "offsets") > > > > > > is something wrong in my expression set? > > > > thank you, > > Saurin > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > ------------------------------------- > Wolfgang Huber > European Bioinformatics Institute > European Molecular Biology Laboratory > Cambridge CB10 1SD > England > Phone: +44 1223 494642 > Http: www.dkfz.de/abt0840/whuber > ------------------------------------- > > ------------------------------------- > Wolfgang Huber > European Bioinformatics Institute > European Molecular Biology Laboratory > Cambridge CB10 1SD > England > Phone: +44 1223 494642 > Http: www.dkfz.de/abt0840/whuber > ------------------------------------- >
ADD REPLY
0
Entering edit mode
Hi Saurin, it seems that the exprSet that in your case comes out of vsn is somehow invalid, but I am not sure why. To debug this, can you please send me the .rda file with esetSub2? (Offline, not to the list). Best wishes Wolfgang <quote who="Saurin Jani"> > Hi Dr. Huber, > > I have done as kept vsn with default TRUE value but I > come up with same error for esetSubNorm[,4:6] > > I have 6 CEL files and I am reading through > Readaffy().I am comparing Knock Out (KO) and Wild > Type(WT) samples from Mouse embryo Fibroblast Affy > data. > > I have below described expression set, please let me > know if you need more values or informatoin for > expression set. > > >> library(vsn); >> library(stam); > >> esetSub2Norm <- vsn(esetSub2); > vsn: 762 x 6 matrix (1 stratum). Please wait for 10 > dots: .......... >> vsnPlotPar(esetSub2Norm, "offsets") > > Here, vsnPlotPar works nice. > > But > >> esetSub2Train <- esetSub2Norm[,4:6]; > Error in validObject(.Object) : Invalid "phenoData" > object: FALSE > >> phenoData(esetSub2); > phenoData object with 3 variables and 6 cases > varLabels > sample: arbitrary numbering > > >> pData(esetSub2); > sample scanner1 scanner2 > Fib1C-KO1 1 0 KO > Fib1C-KO2 2 0 KO > Fib1C-KO3 3 0 KO > Fib1C-WT1 4 1 WT > Fib1C-WT2 5 1 WT > Fib1C-WT3 6 1 WT > > >> exprs(esetSub2) > > Fib1C-KO1 Fib1C-KO2 Fib1C-KO3 Fib1C-WT1 Fib1C-WT2 > Fib1C-WT3 > > 1415768_a_at 8.240705 8.332744 8.176031 8.949155 > 8.913745 8.858628 > > 1415810_at 7.305646 7.565421 7.219027 6.027602 > 6.098046 5.857212 > > 1415811_at 6.671428 6.625956 6.554472 5.264805 > 5.554093 5.674547 > > and so on.... > > > > Thank you, > Saurin > > > > > --- Wolfgang Huber <huber@ebi.ac.uk> wrote: > >> Hi Saurin, >> >> I answer your questions in reverse order: the error >> message in vsnPlotPar >> results from using the option >> 'describe.preprocessing=FALSE' in the call >> to vsn. If you use that option, the fitted >> parameters are not stored in >> the resulting exprSet, hence there is nothing to >> plot for vsnPlotPar. >> >> Second, what happens if you do esetSub2[,4:6]? >> And what happens if you call vsn with >> describe.preprocessing=TRUE (i.e. >> the default)? >> >> If the problem persists, please make the exprSet >> available so I can have a >> look. >> >> Bw >> Wolfgang >> >> <quote who="Saurin Jani"> >> > Hi, >> > >> > I am using R-2.0 with develOK=TRUE. Here, esetSub2 >> is >> > my differentially expressed gene expression set. >> > >> >>esetSub2X <- getIntensityMatrix(esetSub2); >> > >> >>esetSub2Norm <- >> vsn(esetSub2,describe.preprocessing = >> > >> > FALSE); >> > vsn: 762 x 6 matrix (1 stratum). Please wait for >> 10 >> > dots: .......... >> > >> >> esetSub2Train <- esetSub2Norm[,4:6]; >> > Error in validObject(.Object) : Invalid >> "phenoData" >> > object: FALSE >> > >> >> traceback(); >> > 7: stop(paste("Invalid \"", Class, "\" object: ", >> > errors, sep = "")) >> > 6: validObject(.Object) >> > 5: initialize(value, ...) >> > 4: initialize(value, ...) >> > 3: new("phenoData", pData = pD, varLabels = vL) >> > 2: phenoData(x)[j, , ..., drop = FALSE] >> > 1: esetSub2Norm[, 4:6] >> > >> >> vsnPlotPar(esetSub2Norm, "factors") >> > Error in vsnPlotPar(esetSub2Norm, "factors") : >> > 'ny' does not seem to be resulting from >> vsn. >> > >> >> vsnPlotPar(esetSub2Norm, "offsets") >> > Error in vsnPlotPar(esetSub2Norm, "offsets") : >> > 'ny' does not seem to be resulting from >> vsn. >> > >> >> traceback(); >> > 2: stop("'ny' does not seem to be resulting from >> > vsn.") >> > 1: vsnPlotPar(esetSub2Norm, "offsets") >> > >> > >> > is something wrong in my expression set? >> > >> > thank you, >> > Saurin >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor@stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > >> >> >> ------------------------------------- >> Wolfgang Huber >> European Bioinformatics Institute >> European Molecular Biology Laboratory >> Cambridge CB10 1SD >> England >> Phone: +44 1223 494642 >> Http: www.dkfz.de/abt0840/whuber >> ------------------------------------- >> >> ------------------------------------- >> Wolfgang Huber >> European Bioinformatics Institute >> European Molecular Biology Laboratory >> Cambridge CB10 1SD >> England >> Phone: +44 1223 494642 >> Http: www.dkfz.de/abt0840/whuber >> ------------------------------------- >> > > > > > > __________________________________ > Do you Yahoo!? > Yahoo! Mail - You care about security. So do we. > http://promotions.yahoo.com/new_mail > ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Http: www.dkfz.de/abt0840/whuber
ADD REPLY

Login before adding your answer.

Traffic: 357 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6