DESeq teething problems/errors

[Gordona]

Hi there,
I've installed R (version 3.1.10) and DESeq(1.16.0) yesterday.
I've got my counts table and experimental design in, but when I try to estimateSizeFactors I get the following error:

> cds = estimateSizeFactors ( cds )
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘estimateSizeFactors’ for signature ‘"standardGeneric"’

When I ran
> head(cds)

1 structure(function (object, ...)
2 standardGeneric("estimateSizeFactors"), generic = structure("estimateSizeFactors", package = "BiocGenerics"), package = "BiocGenerics", group = list(), valueClass = character(0), signature = "object", default = `\\001NULL\\001`, skeleton = (function (object,
3 ...)
4 stop("invalid call in method dispatch to 'estimateSizeFactors' (no default method)",
5 domain = NA))(object, ...), class = structure("standardGeneric", package = "methods"))


Is there something glaringly obvious that I've done wrong? I've been working through the vignette but substituting my data in instead..
Any help appreciated
Anna

[Simon Anders]

Please always post the complete code, not just the last line that gave the error. Here, for example, the issue is that the variable 'cds' does not contain what it should. So, how have assigned to it further up?

More importantly, though: We keep the old DESeq package around only for the benefit of users who have already established their workflows. As you are just starting anyway, please use DESeq2, not DESeq!

[Gordona]

Same data in R studio worked

Just thought i'd give an update to my earlier post

..i've just put exactly the same data and code into R studio after installing the DESeq package and it's worked and given me the library size.
Sometimes working with R drives me slightly potty!!

[Gordona]

Dear Simon,

Thanks for the advice, will get DESeq2 now.. and i'm sure i'll post again (with full info pasted in)

Anna