[Bioc-sig-seq] edgeR plots for paired samples

Gordon K Smyth smyth at wehi.EDU.AU
Thu Nov 4 00:29:38 CET 2010


Dear Mayte,

> Date: Wed, 3 Nov 2010 10:56:42 -0400
> From: Mayte Suarez-Farinas <farinam at mail.rockefeller.edu>
> To: bioc-sig-sequencing at r-project.org
> Subject: [Bioc-sig-seq] edgeR plots for paired samples
> Message-ID: <C31BCD6A-A0E8-4189-926B-1760F63D64FC at rockefeller.edu>
> Content-Type: text/plain
>
> Dear Bioc
>
> I am using edgeR for paired samples and I am having difficulties with 
> both plotSmear and plotMeanVar functions. I dont know if those functions 
> simply do not work on those cases
>
> PScounts <-readDGE(files.pheno)
> d.PS <- calcNormFactors(PScounts)
> dr.PS <- d.PS[rowSums(d.PS$counts) > 9, ]
> dr.PS.c <- estimateCRDisp(dr.PS, design)
> glmfit.PS.c <- glmFit(dr.PS.c, design, dispersion = dr.PS.c
> $CR.common.dispersion)
> lrt.PS.c <- glmLRT(dr.PS.c, glmfit.PS.c)
>
> plotMeanVar(dr.PS.tgw, meanvar=meanvar, show.tagwise.vars=TRUE,
> NBline=TRUE, dispersion.method="coxreid")
> Error in xy.coords(x, y, xlabel, ylabel, log) :
>   'x' and 'y' lengths differ
> In addition: Warning messages:
> 1: In meanvar$means^2 * tagwise.dispersion :
>   longer object length is not a multiple of shorter object length
> 2: In meanvar$means + meanvar$means^2 * tagwise.dispersion :
>   longer object length is not a multiple of shorter object length

The object dr.PS.tgw that you pass to plotMeanVar() doesn't appear in any 
of the previous code that you give.  Same with meanvar.  Is it possible 
that you've simply used the wrong object name?  It would be normal to pass 
to plotMeanVar your data object such as d.PS or dr.PS.

Best wishes
Gordon

> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] limma_3.6.0          PGSEA_1.20.0         hgu133plus2.db_2.4.5
> org.Hs.eg.db_2.4.6   RSQLite_0.9-2
>  [6] DBI_0.2-5            AnnotationDbi_1.12.0 Biobase_2.10.0
> MASS_7.3-8           biomaRt_2.6.0
> [11] edgeR_1.8.0
>
> loaded via a namespace (and not attached):
>  [1] affy_1.28.0           affyio_1.18.0
> annotate_1.28.0       Biostrings_2.18.0     gcrma_2.22.0
>  [6] genefilter_1.32.0     IRanges_1.8.0
> preprocessCore_1.12.0 RCurl_1.4-3           simpleaffy_2.26.0
> [11] splines_2.12.0        survival_2.35-8       tools_2.12.0
> XML_3.2-0             xtable_1.5-6
> >
> Mayte Suarez-Farinas
> Research Associate, The Rockefeller University
> Biostatistician, The Rockefeller University Hospital
> 1230 York Ave, Box 178,
> New York, NY, 10065
> +1(212) 327-8213


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