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
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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