Hi

I am trying to use the Deseq2paper(V1.3) ‘s calculation about "Shrinkage of dispersion estimates". However, I was stuck even at the beginning (the fifth line of the codes of dispShrink.Rnw)

> library("DESeq2")
> library("DESeq2paper")
> data("pickrell_sumexp")
> idx <- 1:5
> ddsP <- DESeqDataSetFromMatrix(assay(pickrell)[,idx], 
+                                DataFrame(colData(pickrell)[idx,]), ~ 1)
Error in names(x) : 
  no slot of name "NAMES" for this object of class "SummarizedExperiment"

I am trying to figure out the problem, it seems that the problem comes from the Rdata file in the package: pickrell_sumexp.RData. My computer could read it, but only get a empty object, that is the information I get:

    An object of class "SummarizedExperiment"
<S4 Type Object>
attr(,"rowData")
GRangesList object of length 56299:
$ENSG00000000003
GRanges object with 17 ranges and 2 metadata columns:
       seqnames            ranges strand |   exon_id   exon_name
          <Rle>         <IRanges>  <Rle> | <integer> <character>
   [1]        X 99883667-99884983      - |    433098        <NA>
   [2]        X 99884765-99884983      - |    433099        <NA>
   [3]        X 99885756-99885863      - |    433100        <NA>
   [4]        X 99887482-99887565      - |    433101        <NA>
   [5]        X 99887538-99887565      - |    433102        <NA>
   ...      ...               ...    ... .       ...         ...
  [13]        X 99891188-99891686      - |    433110        <NA>
  [14]        X 99891605-99891803      - |    433111        <NA>
  [15]        X 99891605-99891848      - |    433112        <NA>
  [16]        X 99891790-99892101      - |    433113        <NA>
  [17]        X 99894942-99894988      - |    433114        <NA>
  -------
  seqinfo: 101 sequences (1 circular) from an unspecified genome; no seqlengths

...
<56298 more elements>
attr(,"assays")
An object of class "ShallowSimpleListAssays"
<S4 Type Object>
attr(,".xData")
<environment: 0x000000001ec53408>
attr(,"exptData")
List of length 1
attr(,"colData")
DataFrame with 69 rows and 0 columns
Warning message:
In show_GenomicRangesList(object) :
  Note that starting with BioC 3.7, the class attribute of all
  GRangesList **instances** needs to be set to "CompressedGRangesList".
  Please update this object with 'updateObject(object, verbose=TRUE)' and
  re-serialize it.

I have no idea what I should do, is the pickrell_sumexp.RData file damaged in the package? Or have I done something wrong (but I only pasted 5 lines codes)? Or is there anything wrong in my computer?

Thank you very much in advance.

I encountered this problem as well. The data is available but updateObject doesn't work and it's tricky to find how the data are stashed.

I updated these objects and posted bottomly on the apeglmPaper repo 2 years ago, I've now added pickrell:

https://github.com/mikelove/apeglmPaper/tree/master/sim/rdata