Question: Deseq Handle Samples Without Replicates
2
gravatar for camelbbs
6.6 years ago by
camelbbs650
China
camelbbs650 wrote:

I've tried the package DESeq and want to apply in our datasets: two samples without replicates.

I first summarized the counts in a table: brain liver uc001aaa.3 0 0 uc001aac.4 0 0 uc001aae.4 0 0 ... ...

By following code:

over<-read.table("wokao.txt",header=T,row.names=1)
conds<-c("brain","liver")
cds<-newCountDataSet(over,conds)
cds<-estimateSizeFactors(cds)
cds<-estimateDispersions(cds,method="blind",sharingMode="fit-only")

Error in parametricDispersionFit(means, disps) :

Parametric dispersion fit failed. Try a local fit and/or a pooled estimation. (See '?estimateDispersions')

cds2=cds[,c("brain","liver")]
cds2=estimateSizeFactors(cds2)
cds2=estimateDispersions(cds2,method="blind",sharingMode="fit-only")

Error in parametricDispersionFit(means, disps) :

Parametric dispersion fit failed. Try a local fit and/or a pooled estimation. (See '?estimateDispersions')

I have no idea why there is the error. May you give some guides.

sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale: [1] LCCOLLATE=EnglishUnited States.1252 LCCTYPE=EnglishUnited States.1252 LCMONETARY=EnglishUnited States.1252 [4] LCNUMERIC=C LCTIME=English_United States.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] DESeq1.8.3 locfit1.5-8 Biobase2.16.0 BiocGenerics0.2.0

loaded via a namespace (and not attached): [1] annotate1.34.1 AnnotationDbi1.18.4 DBI0.2-5 genefilter1.38.0 geneplotter1.34.0
[6] grid
2.15.1 IRanges1.14.4 lattice0.20-10 RColorBrewer1.0-5 RSQLite0.11.2
[11] splines2.15.1 stats42.15.1 survival2.36-14 XML3.95-0.1 xtable_1.7-0

deseq rna-seq • 6.0k views
ADD COMMENTlink modified 6.6 years ago by earonesty220 • written 6.6 years ago by camelbbs650
1

Please update your question by pasting in the output of sessionInfo() after the DESeq package has been loaded. It is also suggesting that you try a local fit for your estimation, so why not try that? Look in ?estimateDispersions to figure out how.

ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by Steve Lianoglou5.0k

Thanks, But I don't know how to use local fit in this code

ADD REPLYlink written 6.6 years ago by camelbbs650

While I add cds<-estimateDispersions(cds,method="blind",sharingMode="fit-only",fitType="local") It works and can be used in res<-nbinomTest(cds,"brain","liver")

Is that right?

ADD REPLYlink written 6.6 years ago by camelbbs650

For what definition of "right"? I mean, it seems to "work", so ... what else can I tell you? Without any replicates, it's hard to say that something is right.

I'm curious why the other approach fails, though. You might want to upgrade to the latest release of bioconductor (and its related packages). The current release of DESeq is 1.10.1. The very top of the Bioconductor Install Page shows how to upgrade to Bioconductor 2.11:

source("http://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")
ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by Steve Lianoglou5.0k

Thanks a lot. ~~

ADD REPLYlink written 6.6 years ago by camelbbs650

Hint: when you begin lines in your question with ">", it's formatted as a blockquote; probably not what you want. Instead, prefix lines of code with 4 spaces. Fixed it for you.

ADD REPLYlink written 6.6 years ago by Neilfws48k
0
gravatar for earonesty
6.6 years ago by
earonesty220
United States
earonesty220 wrote:

edgeR handles samples without replicates well, but the question is why? Unless you are looking at platform technical variation, you won't find any biologically meaningful results.

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by earonesty220
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