Entering edit mode
deepika lakhwani
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170
@deepika-lakhwani-5470
Last seen 10.3 years ago
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.
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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