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]]

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

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

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]]