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Question: DESEQ problem
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gravatar for Dawei Li
6.2 years ago by
Dawei Li50
Dawei Li50 wrote:
Dear simon: I used your program to process the count data. I got the following message when I generate the plott: > smoothScatter( log10(diagForIC$baseMean), log10(diagForIC$baseVar) ) KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Error in if (!missing(bandwidth) && min(bandwidth) <= 0) stop("'bandwidth' must be strictly positive") :   missing value where TRUE/FALSE needed Calls: smoothScatter -> <anonymous> -> <anonymous> In addition: Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf 3: In min(x) : no non-missing arguments to min; returning Inf 4: In max(x) : no non-missing arguments to max; returning -Inf Execution halted Please give me some advice. dawei li [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Dawei Li50
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gravatar for Steve Lianoglou
6.2 years ago by
Genentech
Steve Lianoglou12k wrote:
Hi Dawei, I'm not sure what the problem is myself, but to help facilitate you getting an answer from those who might now what's happening, I suggest you provide the output of sessionInfo() when DESeq is loaded, so that we can see what versions of DESeq (and R) you are running. -steve On Mon, Sep 19, 2011 at 9:51 AM, Dawei Li <dawei_lili at="" yahoo.com=""> wrote: > Dear simon: > > I used your program to process the count data. I got the following message when I generate the plott: >> smoothScatter( log10(diagForIC$baseMean), log10(diagForIC$baseVar) ) > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > Error in if (!missing(bandwidth) && min(bandwidth) <= 0) stop("'bandwidth' must be strictly positive") : > ? missing value where TRUE/FALSE needed > Calls: smoothScatter -> <anonymous> -> <anonymous> > In addition: Warning messages: > 1: In min(x) : no non-missing arguments to min; returning Inf > 2: In max(x) : no non-missing arguments to max; returning -Inf > 3: In min(x) : no non-missing arguments to min; returning Inf > 4: In max(x) : no non-missing arguments to max; returning -Inf > Execution halted > > > Please give me some advice. > > dawei li > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENTlink written 6.2 years ago by Steve Lianoglou12k
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gravatar for Simon Anders
6.2 years ago by
Simon Anders3.4k
Zentrum für Molekularbiologie, Universität Heidelberg
Simon Anders3.4k wrote:
Hi On 09/19/2011 03:51 PM, Dawei Li wrote: > Dear simon: > I used your program to process the count data. I got the following > message when I generate the plott: > > > smoothScatter( log10(diagForIC$baseMean), log10(diagForIC$baseVar) ) [...] > Error in if (!missing(bandwidth) && min(bandwidth) <= 0) [..] It is a bit hard to diagnose this without further information. Please try two things. Have a look at 'head(diagForIC)'. Maybe something looks unusual there. Then, try to plot without the kernel density estimation of smoothScatter: plot( log10(diagForIC$baseMean), log10(diagForIC$baseVar), pch="." ) How does this look lie? Simon
ADD COMMENTlink written 6.2 years ago by Simon Anders3.4k
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gravatar for Dawei Li
6.2 years ago by
Dawei Li50
Dawei Li50 wrote:
Dear simon: Can you see what is the following problem: cds   <- estimateVarianceFunctions(cds,method=TRUE) Error: could not find function "estimateDispersions" I did reinstall the DESEQ package using the following command: source("http://www.bioconductor.org/biocLite.R") biocLite("DESeq") what is the problem? dawei li [[alternative HTML version deleted]]
ADD COMMENTlink written 6.2 years ago by Dawei Li50
Dear Simon:  The following is my code: library("DESeq") countsTable<-read.table("mycount.dat", sep = "\t",header=TRUE, stringsAsFactors=TRUE, row.names="gene") conds <- factor(c("T","C")) cds   <- newCountDataSet( countsTable, conds ) cds   <- estimateSizeFactors( cds) cds   <- estimateVarianceFunctions(cds,method=TRUE) I got the following error message: Error in match.arg(method) : 'arg' must be NULL or a character vector dawei li [[alternative HTML version deleted]]
ADD REPLYlink written 6.2 years ago by Dawei Li50
Hi Dawei, The error message is pretty clear. You said method=TRUE and it's unhappy with that. A look at the help for that function (?estimateVarianceFunctions) would tell you what arguments are acceptable for the method. Francois On Sep 28, 2011, at 10:12 , Dawei Li wrote: > > Dear Simon: > > > The following is my code: > > library("DESeq") > countsTable<-read.table("mycount.dat", sep = "\t",header=TRUE, stringsAsFactors=TRUE, row.names="gene") > conds <- factor(c("T","C")) > cds <- newCountDataSet( countsTable, conds ) > cds <- estimateSizeFactors( cds) > cds <- estimateVarianceFunctions(cds,method=TRUE) > > I got the following error message: > > Error in match.arg(method) : 'arg' must be NULL or a character vector > > dawei li > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.2 years ago by Francois Pepin80
Hi, On Wed, Sep 28, 2011 at 1:12 PM, Dawei Li <dawei_lili at="" yahoo.com=""> wrote: > > Dear Simon: > > > ?The following is my code: > > library("DESeq") > countsTable<-read.table("mycount.dat", sep = "\t",header=TRUE, stringsAsFactors=TRUE, row.names="gene") > conds <- factor(c("T","C")) > cds?? <- newCountDataSet( countsTable, conds ) > cds?? <- estimateSizeFactors( cds) > cds?? <- estimateVarianceFunctions(cds,method=TRUE) > > I got the following error message: > > Error in match.arg(method) : 'arg' must be NULL or a character vector I suspect this is because of the value you are giving for the `method` argument to `estimateVarianceFunctions`. Take a closer look at the help from ?estimateVarianceFunctions ... it doesn't seem like "TRUE" is a valid value for that argument. This is true for my version of DESeq, though (1.4.1) -- you still haven't given us the output of sessionInfo() so it's making it difficult to diagnose your problems ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD REPLYlink written 6.2 years ago by Steve Lianoglou12k
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