On Wed, Oct 6, 2010 at 10:46 PM, ANJAN PURKAYASTHA <anjan.purkayastha at="" gmail.com=""> wrote: > Vince, > Thanks. So it looks like there is no way for me to use expresso to perform > background correction, normalization and then examine the data before > proceeding to other downstream analyses. > Any suggestions on how I can accomplish this without the help of expresso? You can perform standalone background correction using the bg.correct.* functions You can perform normalization at the probe intensity level using the normalize.AffyBatch.* functions these accept and return AffyBatch instances; you can get the intensity measures at any stage using, say, pm() it seems you want to avoid the summarization to an expression value to "examine the data"; expresso expressly wants to do a summarization to an expression value, so don't use it, but use the components separately. > Thanks, > Anjan > > On Wed, Oct 6, 2010 at 10:32 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> > wrote: >> >> I reproduced your experience. ?The problem is that the software lets >> you get away >> with not specifying the summary.method and the pmcorrect.method at the >> interface, but >> when it gets around to doing the expression computations, if it gets >> NULLs (the default) >> it dies. ?expresso() should probably force the user to put something >> in or put reasonable >> defaults. >> >> if you add summary.method = "avgdiff" and pmcorrect.method="pmonly" to >> your call, for example, >> it will complete. ?you have to look over the options for those >> methods; the doc is not crystal >> clear in all places. ?for some parameters function calls will tell you >> the options available >> >> > bgcorrect.methods() >> [1] "bg.correct" "mas" ? ? ? ?"none" ? ? ? "rma" >> > pmcorrect.methods() >> [1] "mas" ? ? ? ?"methods" ? ?"pmonly" ? ? "subtractmm" >> >> summary.methods() does not seem to exist. ?but >> >> > generateExprSet.methods() >> [1] "avgdiff" ? ? ?"liwong" ? ? ? "mas" ? ? ? ? ?"medianpolish" >> "playerout" >> >> seems to supply the relevant options for that parameter. >> >> >> On Wed, Oct 6, 2010 at 9:59 PM, ANJAN PURKAYASTHA >> <anjan.purkayastha at="" gmail.com=""> wrote: >> > Hi Vincent, >> > I used the Mouse Genome 430 2.0 Array >> > >> > (http://www.affymetrix.com/support/technical/byproduct.affx?produ ct=moe430-20) >> > >> > Here is my session info: >> > R version 2.11.1 (2010-05-31) >> > i386-apple-darwin9.8.0 >> > >> > locale: >> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> > >> > attached base packages: >> > [1] stats???? graphics? grDevices utils???? datasets? methods?? base >> > >> > other attached packages: >> > [1] mouse4302cdf_2.6.0 simpleaffy_2.24.0? gcrma_2.20.0 >> > genefilter_1.30.0? affy_1.26.1??????? Biobase_2.8.0 >> > >> > loaded via a namespace (and not attached): >> > ?[1] affyio_1.16.0???????? annotate_1.26.1?????? AnnotationDbi_1.10.2 >> > Biostrings_2.16.9???? DBI_0.2-5???????????? IRanges_1.6.17 >> > preprocessCore_1.10.0 >> > ?[8] RSQLite_0.9-2???????? splines_2.11.1??????? survival_2.35-8 >> > tools_2.11.1????????? xtable_1.5-6 >> > >> > Thanks in advance for your help. >> > Anjan >> > >> > >> > On Wed, Oct 6, 2010 at 9:36 PM, Vincent Carey >> > <stvjc at="" channing.harvard.edu=""> >> > wrote: >> >> >> >> please provide your sessionInfo() and the specific class of array in >> >> use -- there are various mouse >> >> expression arrays from affy. >> >> >> >> On Wed, Oct 6, 2010 at 9:17 PM, ANJAN PURKAYASTHA >> >> <anjan.purkayastha at="" gmail.com=""> wrote: >> >> > Hi, >> >> > I have created an affybatch object from 3 cel files. The files have >> >> > data >> >> > from Affymetrix's Mouse Expression (Oligonucleotide) array. >> >> > Affybatch object was created by command: >> >> > testAffy <- ReadAffy() >> >> > >> >> > In the next step I tried to use expresso to adjust background using >> >> > RMA >> >> > and >> >> > normalize using loess, using the command: >> >> > testAffy.loess = expresso(testAffy, bgcorrect.method= "rma", >> >> > normalize.method= "loess") >> >> > Here is the output: >> >> > background correction: rma >> >> > normalization: loess >> >> > PM/MM correction : >> >> > expression values: >> >> > background correcting...done. >> >> > normalizing...Done with 1 vs 2 in iteration 1 >> >> > Done with 1 vs 3 in iteration 1 >> >> > Done with 2 vs 3 in iteration 1 >> >> > 1 0.0176947 >> >> > done. >> >> > Error in function (classes, fdef, mtable) ?: >> >> > ?unable to find an inherited method for function "computeExprSet", >> >> > for >> >> > signature "AffyBatch", "NULL", "NULL" >> >> > >> >> > The testAffy.loess object was not created. ?Any idea why I am getting >> >> > an >> >> > error on running the expresso command? >> >> > Thanks in advance. >> >> > Anjan >> >> > >> >> > -- >> >> > =================================== >> >> > anjan purkayastha, phd. >> >> > research associate >> >> > fas center for systems biology, >> >> > harvard university >> >> > 52 oxford street >> >> > cambridge ma 02138 >> >> > phone-703.740.6939 >> >> > =================================== >> >> > >> >> > ? ? ? ?[[alternative HTML version deleted]] >> >> > >> >> > _______________________________________________ >> >> > Bioconductor mailing list >> >> > Bioconductor at stat.math.ethz.ch >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > Search the archives: >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >> > >> > >> > >> > -- >> > =================================== >> > anjan purkayastha, phd. >> > research associate >> > fas center for systems biology, >> > harvard university >> > 52 oxford street >> > cambridge ma 02138 >> > phone-703.740.6939 >> > =================================== >> > > > > > -- > =================================== > anjan purkayastha, phd. > research associate > fas center for systems biology, > harvard university > 52 oxford street > cambridge ma 02138 > phone-703.740.6939 > =================================== >