Hi,
I´m a little puzzled about the 'Dierential analysis of count data : the
DESeq2 package' protocol
I was trying it with (only) two samples and got the DE results, then I tried the suggested transformations:
(being 'des' my previous results, just as it appears in the 'manual')
dseBlind <- dse
design(dseBlind) <- formula(~ 1)
dseBlind <- estimateDispersions(dseBlind)
rld <- rlogTransformation(dseBlind)
vsd <- varianceStabilizingTransformation(dseBlind)
At this point I had assumed that the 'rld' and 'vsd' objects are like 'dse' but with the transformations, however when I try to retrieve the results I get:
> Prueba.rld.res <- results(rld)
Error in tail(all.vars(design(object)), 1) :
error in evaluating the argument 'x' in selecting a method for function 'tail': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘design’ for signature ‘"SummarizedExperiment"’
Am I missing something, should I instead use the 'rld' or 'vsd' objects with my DE analysis somehow???
many many thanks!!
I´m a little puzzled about the 'Dierential analysis of count data : the
DESeq2 package' protocol
I was trying it with (only) two samples and got the DE results, then I tried the suggested transformations:
(being 'des' my previous results, just as it appears in the 'manual')
dseBlind <- dse
design(dseBlind) <- formula(~ 1)
dseBlind <- estimateDispersions(dseBlind)
rld <- rlogTransformation(dseBlind)
vsd <- varianceStabilizingTransformation(dseBlind)
At this point I had assumed that the 'rld' and 'vsd' objects are like 'dse' but with the transformations, however when I try to retrieve the results I get:
> Prueba.rld.res <- results(rld)
Error in tail(all.vars(design(object)), 1) :
error in evaluating the argument 'x' in selecting a method for function 'tail': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘design’ for signature ‘"SummarizedExperiment"’
Am I missing something, should I instead use the 'rld' or 'vsd' objects with my DE analysis somehow???
many many thanks!!
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