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Old 04-19-2012, 03:01 AM   #1
Location: shanghai, chia

Join Date: Mar 2009
Posts: 67
Default Problem of New DESeq without any replicates

Recently, I do some RNA-seq analysis. The old version of DESeq do well with the data set without any replicate. However, I came across some error when i ran the newest version following the userguide. Please help.

> cds
CountDataSet (storageMode: environment)
assayData: 49 features, 2 samples
element names: counts
protocolData: none
sampleNames: zhuan L158
varLabels: sizeFactor condition
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
> cds=estimateDispersions(cds, methold="blind", sharingMode='fit-only')
Error in rowSums(sapply(tapply((1:ncol(counts))[replicated_sample], factor(conditions[replicated_sample]), :
'x' must be an array of at least two dimensions
In addition: Warning message:
In .local(object, ...) :
in estimateDispersions: Ignoring extra argument(s).
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Old 04-23-2012, 04:03 PM   #2
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Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438

> cds=estimateDispersions(cds, methold="blind", sharingMode='fit-only')

should be

> cds=estimateDispersions(cds, method="blind", sharingMode='fit-only')

Also try including the fitType setting:

> cds=estimateDispersions(cds, method="blind", sharingMode='fit-only',fitType="local")
sdriscoll is offline   Reply With Quote

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