Thread: DESeq2 error
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Old 09-06-2014, 01:31 PM   #3
stormin
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Location: US

Join Date: Aug 2014
Posts: 23
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Hmm, that didn't work unfortunately. Here is my R script with the same error message. I'm new to R, so sorry in advance if there is a very obvious mistake. Thanks!


Quote:
#!/usr/bin/Rscript

library('DESeq2')

directory <- getwd()
sink("DESeq_output.txt")
sampleTable <- read.csv("sampleTable.csv")

dds <- DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design = ~ condition)
colData(dds)$condition <- relevel(colData(dds)$condition, "noCoverage")
dds <- DESeq(dds, fitType="parametric")
results <- results(dds)
results <- results[order(results$padj), ]
write.csv(results,file="DESeq_results.csv")
sink()

detach("packageESeq2")

quit()
Same error message plus addition 18 warnings:
Quote:
1: In estimateDispersionsFit(object, fitType = fitType, quiet = quiet) :
the parametric fit of dispersion estimates over the mean of counts
failed, which occurs when the trend is not well captured by the
function y = a/x + b. A local regression fit is automatically performed,
and the analysis can continue. You can specify fitType='local' or 'mean'
to avoid this message if re-running the same data.
When using local regression fit, the user should examine plotDispEsts(dds)
to make sure the fitted line is not sharply curving up or down based on
the position of individual points.
2: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
3: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
4: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
5: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
6: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
7: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
8: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
9: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
10: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
11: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
12: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
13: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
14: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
15: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
16: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
17: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
18: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with non-zero weight
Content of the sampleTable.csv
Quote:
sampleName,fileName,condition
2hnoCoverage,counts_Coverage.txt,Coverage
2hCoverage,counts_noCoverage.txt,noCoverage

Last edited by stormin; 09-07-2014 at 09:45 AM.
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