Dear Mayte,
Date: Wed, 3 Nov 2010 10:56:42 -0400
From: Mayte Suarez-Farinas <[email protected]>
To: [email protected]
Subject: [Bioc-sig-seq] edgeR plots for paired samples
Message-ID: <[email protected]>
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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