Dear Bioconductors, I would like to use the affy and multtest packages to extract a list of differentially expressed genes from a set of 8 experiments, in which 4 are wildtype and 4 are knockouts. I have worked through several of the affymetric vignettes and the mult test vignette, which are all very well done. However, for some reason, I cannot extract a proper n x m matrix with n= probe sets and m = samples. My steps: library(affy) Data<-ReadAffy() /* Loads 8 .cel files with no error message */ eset <- rma(Data /* also OK */ ex <- exprs(eset) I would like to get a matrix object similar to "golub" from the Vignette. However, there are several differences. Firstly, "ex" has labels for the probe_ids for all genes and does not display as a 12488 x 8 matrix (the output of dim(ex), but rather as a (12488x8) x 2 matrix in which the first column is the probe id and the second column is the expression level. Also, there is no separate attribute such as golub.gnames. Several of the downstream analyses as described in the multtest vignette do not work properly, but I assume that the main problem is here. Any ideas? Thanks Peter

=> Ken, thanks. My main difficulty, which presumably comes from lack of sufficient experience with bioconductor, is that the object ex appeared to be different from the matrix object "golub", which is a matrix instance used in the vignette for the multtest package. This instance also has the attributes golub.gnames and golub.cl (a vector of tumor class labels). Also, the golub does not appear to have rownames as an attribute (presumably because it has .gnames). So, I had assumed that exprs was supposed to return a comparable object. In the meantime, I have managed to get my analyses done (btw, thanks to all who have contributed to bioconductor, it is a truly amazing resource!), but I wound up creating a separate vector for the class labels and probably have done many things "correctly but clumsily". So my question is whether there are settings to create matrix objects with a structure comparable to golub, and if this is the prefered way of working with bioconductor? -Peter Peter, Your object "ex" is just a numeric matrix. (to see this, do: class(ex) and mode(ex).) The row names of your matrix are probe set identifiers (try e.g. rownames(ex)[1:10]). NB: this is not the first column of the matrix. When you say "several of the downstream analyses do not work properly", you should tell us which ones, and what errors you got. Cheers, Ken On Mon, 17 Nov 2003, peter robinson wrote: > Dear Bioconductors, > > I would like to use the affy and multtest packages to extract a list of > differentially expressed genes from a set of 8 experiments, in which 4 are > wildtype and 4 are knockouts. I have worked through several of the affymetric > vignettes and the mult test vignette, which are all very well done. However, > for some reason, I cannot extract a proper n x m matrix with n= probe sets > and m = samples. > My steps: > > library(affy) > Data<-ReadAffy() /* Loads 8 .cel files with no error message */ > eset <- rma(Data /* also OK */ > ex <- exprs(eset) > > I would like to get a matrix object similar to "golub" from the Vignette. > However, there are several differences. Firstly, "ex" has labels for the > probe_ids for all genes and does not display as a 12488 x 8 matrix (the > output of dim(ex), but rather as a (12488x8) x 2 matrix in which the first > column is the probe id and the second column is the expression level. Also, > there is no separate attribute such as golub.gnames. > > Several of the downstream analyses as described in the multtest vignette do > not work properly, but I assume that the main problem is here. > > Any ideas? > > Thanks > > Peter