Member
Location: US
Join Date: Aug 2014
Posts: 23

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 rerunning 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 nonzero weight
3: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
4: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
5: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
6: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
7: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
8: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
9: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
10: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
11: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
12: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
13: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
14: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
15: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
16: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
17: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight
18: In lfproc(x, y, weights = weights, cens = cens, base = base, ... :
procv: no points with nonzero weight

Content of the sampleTable.csv
Quote:
sampleName,fileName,condition
2hnoCoverage,counts_Coverage.txt,Coverage
2hCoverage,counts_noCoverage.txt,noCoverage

Last edited by stormin; 09072014 at 09:45 AM.
