> Date: Mon, 2 Apr 2007 14:23:45 +0100 > From: "Mikhail, Amy" <a.mikhail at="" abdn.ac.uk=""> > Subject: Re: [BioC] "AveExp" column has dissappeared from limma > topTable > To: "Marcus Davy" <mdavy at="" hortresearch.co.nz=""> > Cc: bioconductor at stat.math.ethz.ch > > Hi Marcus, > > "Mosquito" is a subset of my original exprSet (with some probesets taken > out). So it is just a matrix There is no reason why a subset of an exprSet should not be an exprSet also. Just subset the object without using exprs(). Best wishes Gordon > and now that I look, there is no "Amean" > element in my fit object. I didn't know that Amean would not be > derrived for matrices, thanks for pointing that out. > > Many thanks, > Amy

Hi Gordon, Thanks for your reply, just tried subsetting without exprs() and it returned a sub-setted exprSet, as you said... So just wondering, when does one actually need to use exprs() and when can I get away without it? Also, what is the difference between an exprSet and an ExpressionSet? Many thanks, Amy -----Original Message----- From: Gordon K Smyth [mailto:smyth@wehi.EDU.AU] Sent: Tuesday, April 03, 2007 10:56 PM To: Mikhail, Amy Cc: bioconductor at stat.math.ethz.ch Subject: AveExp" column has dissappeared from limma topTable > Date: Mon, 2 Apr 2007 14:23:45 +0100 > From: "Mikhail, Amy" <a.mikhail at="" abdn.ac.uk=""> > Subject: Re: [BioC] "AveExp" column has dissappeared from limma > topTable > To: "Marcus Davy" <mdavy at="" hortresearch.co.nz=""> > Cc: bioconductor at stat.math.ethz.ch > > Hi Marcus, > > "Mosquito" is a subset of my original exprSet (with some probesets > taken out). So it is just a matrix There is no reason why a subset of an exprSet should not be an exprSet also. Just subset the object without using exprs(). Best wishes Gordon > and now that I look, there is no "Amean" > element in my fit object. I didn't know that Amean would not be > derrived for matrices, thanks for pointing that out. > > Many thanks, > Amy

Hi Amy, "Mikhail, Amy" <a.mikhail at="" abdn.ac.uk=""> writes: > Thanks for your reply, just tried subsetting without exprs() and it > returned a sub-setted exprSet, as you said... So just wondering, when > does one actually need to use exprs() and when can I get away without > it? Many Bioconductor packages have methods defined for ExpressionSet objects and for these, you don't need to extract the matrix using exprs(). Whenever you have a function that expects a matrix as its argument and not an ExpressionSet object, then you use exprs(). > Also, what is the difference between an exprSet and an > ExpressionSet? exprSet and ExpressionSet are both classes used to represent microarray data. exprSet is now deprecated in favor of ExpressionSet. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

Hi Seth and Gordon, >> Also, what is the difference between an exprSet and an ExpressionSet? >exprSet and ExpressionSet are both classes used to represent microarray data. exprSet is now deprecated in favor of ExpressionSet. >+ seth In a previous post, Gordon has said: "If the first argument to lmFit() is an MAList or exprSet or ExpressionSet then Amean is computed. It is actually not clear that this is right behaviour in the case of an ExpressionSet, but that's how it is for now." So, that's what made me wonder what is the specific difference between exprSet and ExpressionSets that would make Amean a sensible thing to extract in the first case but not necessarily in the second? Many thanks, Amy

On Thu, April 5, 2007 11:31 pm, Mikhail, Amy wrote: > -----Original Message----- > From: Mikhail, Amy > Sent: Thursday, April 05, 2007 2:30 PM > To: 'Seth Falcon' > Cc: bioconductor at stat.math.ethz.ch > Subject: RE: [BioC] AveExp" column has dissappeared from limma topTable > > Hi Seth and Gordon, > >>> Also, what is the difference between an exprSet and an ExpressionSet? > >>exprSet and ExpressionSet are both classes used to represent microarray > data. exprSet is now deprecated in favor of ExpressionSet. > >>+ seth > > In a previous post, Gordon has said: > "If the first argument to lmFit() is an MAList or exprSet or > ExpressionSet then Amean is computed. It is actually not clear that this > is right behaviour in the case of an ExpressionSet, but that's how it is > for now." > > So, that's what made me wonder what is the specific difference between > exprSet and ExpressionSets that would make Amean a sensible thing to > extract in the first case but not necessarily in the second? > > Many thanks, > Amy Amy, I'm not an ExpressionSet developer, and you can read the documentation as easily as I can (have you done that?), but ExpressionSet seems to have more general intent than exprSet. ExpressionSet seems intended to contain any sort of expression data at all, and that could conceivably mean log-ratios instead of log-intensities, and hence how would you compute average intensities? I suspect that in practice ExpressionSet, like exprSet, will be most commonly be used for Affy and Illumina data, hence the expression values will virtually always be log-intensities. As you are using Affymetrix data, so you will never have to worry about any of this. Gordon