Hi,

On Wednesday, August 29, 2012, deepika lakhwani wrote:

> hello....
>
> i am trying ti find out differential gene by the edgeR package.i have 2
> transcriptome libraries, one is control and other is experimental.


There is a section in the edgeR user guide that deals with the scenario
where you do not have any replicates (which is the situation you seem to be
in)

Follow the instructions there.

HTH

-steve

> when i estimate overall dispersion for the dataset.  its gives me warning
> message:
>
> Warning message:
> In estimateGLMCommonDisp.default(y = y$counts, design = design,  :
>   No residual df: setting dispersion to NA
>
> and without dispersion value, i can not find DE genes.now what i do?please
> anyone tell me.
>
> these are the commands:
>
> rawdata1 <- read.delim("banana.txt", check.names=FALSE,
> stringsAsFactors=FALSE)
> > head(rawdata)
>               0day ethy
> 1 contig00001  625  115
> 2 contig00002  662   88
> 3 contig00003  466  563
> 4 contig00004  610   98
> 5 contig00005   72   21
> 6 contig00006   82    2
> > library(edgeR)
> > y <- DGEList(counts=rawdata[,2:3], genes=rawdata[,1:1])
> Calculating library sizes from column totals.
> > y <- calcNormFactors(y)
> > y$samples
>      group lib.size norm.factors
> 0day     1    34450    1.1292933
> ethy     1    25198    0.8855096
> > plotMDS(y)
> Error in cmdscale(as.dist(dd), k = ndim) :
>   'k' must be in {1, 2, ..  n - 1}
> > Patient <- factor(c(0,1))
> > Tissue <- factor(c("N","T"))
> > data.frame(Sample=colnames(y),Patient,Tissue)
>   Sample Patient Tissue
> 1   0day       0      N
> 2   ethy       1      T
> > design <- model.matrix(~Patient+Tissue)
> > rownames(design) <- colnames(y)
> > y <- estimateGLMCommonDisp(y, design, verbose=TRUE)
> Warning message:
> In estimateGLMCommonDisp.default(y = y$counts, design = design,  :
>   No residual df: setting dispersion to NA
> > y <- estimateGLMCommonDisp(y)
> > y <- estimateGLMTrendedDisp(y)
> > y <- estimateGLMTagwiseDisp(y)
> Warning message:
> In movingAverageByCol(apl[o, ], width = 1000) :
>   reducing moving average width to nrow(x)
> > fit <- glmFit(y, design)
> Error in beta[i, ] <- z %*% X :
>   number of items to replace is not a multiple of replacement length
> > rawdata1 <- read.delim("banana.txt", check.names=FALSE,
> stringsAsFactors=FALSE)
> >  library(edgeR)
> > y <- DGEList(counts=rawdata[,2:3], genes=rawdata[,1:1])
> Calculating library sizes from column totals.
> >  y <- calcNormFactors(y)
> >  y$samples
>      group lib.size norm.factors
> 0day     1    34450    1.1292933
> ethy     1    25198    0.8855096
> >  plotMDS(y)
> Error in cmdscale(as.dist(dd), k = ndim) :
>   'k' must be in {1, 2, ..  n - 1}
>
>
>
> please help me.
>
> regards
> deepika
>
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>
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-- 
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

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