Hi,
I installed the DEseq version 1.0.6 from the repository to my mac, and am trying to use the example provided in the vignettes:
library("DESeq")
countsTable <- read.delim(system.file("extra/TagSeqExample.tab", package="DESeq"), header=TRUE, stringsAsFactors=TRUE, row.names="gene")
conds <- factor(c("T", "T", "T", "Tb", "N", "N"))
cds <- newCountDataSet( countsTable, conds )
cds <- estimateSizeFactors( cds )
cds <- estimateVarianceFunctions( cds )
res <- nbinomTest( cds, "T", "N")
every command seemed to work until it hits nbinomTest(), where I get an error: attempt to apply non-function. However when I type help(nbinomTest), the documentation of this function does pop up. Does anyone experience the same problem?
Also, when I checked what the variable cds is after applying estimateVarianceFunctions( cds ), I get the following output, is this normal???
Thank you so much!
> cds
CountDataSet (storageMode: environment)
assayData: 18760 features, 6 samples
element names: counts
protocolData: none
phenoData
sampleNames: T1a, T1b, ..., N2 (6 total)
varLabels and varMetadata description:
condition: NA
sizeFactor: NA
featureData: none
experimentData: use 'experimentData(object)'
Annotation:
I installed the DEseq version 1.0.6 from the repository to my mac, and am trying to use the example provided in the vignettes:
library("DESeq")
countsTable <- read.delim(system.file("extra/TagSeqExample.tab", package="DESeq"), header=TRUE, stringsAsFactors=TRUE, row.names="gene")
conds <- factor(c("T", "T", "T", "Tb", "N", "N"))
cds <- newCountDataSet( countsTable, conds )
cds <- estimateSizeFactors( cds )
cds <- estimateVarianceFunctions( cds )
res <- nbinomTest( cds, "T", "N")
every command seemed to work until it hits nbinomTest(), where I get an error: attempt to apply non-function. However when I type help(nbinomTest), the documentation of this function does pop up. Does anyone experience the same problem?
Also, when I checked what the variable cds is after applying estimateVarianceFunctions( cds ), I get the following output, is this normal???
Thank you so much!
> cds
CountDataSet (storageMode: environment)
assayData: 18760 features, 6 samples
element names: counts
protocolData: none
phenoData
sampleNames: T1a, T1b, ..., N2 (6 total)
varLabels and varMetadata description:
condition: NA
sizeFactor: NA
featureData: none
experimentData: use 'experimentData(object)'
Annotation:
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