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  • 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
    phenoData
    sampleNames: zhuan L158
    varLabels: sizeFactor condition
    varMetadata: labelDescription
    featureData: none
    experimentData: use 'experimentData(object)'
    Annotation:
    > 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).

  • #2
    > 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")
    /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
    Salk Institute for Biological Studies, La Jolla, CA, USA */

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