Hi. On Thu, Nov 18, 2010 at 9:40 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: > > Dear all, > > I’m trying to solve my copynumber segmentation problem using aroma > affymetrix, according to the Vignette > > I created a folder : rawData ,under my working directory, and inside that > folder I created another folder Mapping50K_Hind240 , inside which I put my > 600ish .cel file > > Isn’t it correct?
No. You missed that you need a data set directory to under rawData, e.g. rawData/NameOfMyDataSet/Mapping50K_Hind240/. See for instance page 'Setup: Quick Summary Of Required File Structure' [http://aroma-project.org/node/79]. See also http://aroma-project.org/setup/. > > > > Then I did : > > > > ds <- doCRMAv1("R:/work/breast/breast data files/MYC/rawData", > chipType="Mapping50K_Hind240") You should never have to specify a path/directory when using the aroma framework, instead it should look something like: ds <- doCRMAv1("NameOfMyDataSet", chipType="Mapping50K_Hind240"); Since the aroma framework nows where to look for data files, it is all automagically taken care of. Hope this helps Henrik > > > > (“R:/work/breast/breast data files/MYC/” is my working directory) > > > > Why I got the error message: > > > > Error in list(`doCRMAv1("R:/work/breast/breast data files/MYC/rawData", > chipType = "Mapping50K_Hind240")` = <environment>, : > > > > [2010-11-18 16:41:10] Exception: Could not locate a file for this chip type: > Mapping50K_Hind240 > > at throw(Exception(...)) > > at throw.default("Could not locate a file for this chip type: ", > paste(c(chipType, tags), collapse = ",")) > > at throw("Could not locate a file for this chip type: ", paste(c(chipType, > tags), collapse = ",")) > > at method(static, ...) > > at AffymetrixCdfFile$byChipType(chipType) > > at method(static, ...) > > at AffymetrixCelSet$byName(dataSet, ..., verbose = less(verbose, 50), > .onUnknownArgs = "ignore") > > at doCRMAv1.character("R:/work/breast/breast data files/MYC/rawData", > chipType = "Mapping50K_Hind240") > > at doCRMAv1("R:/work/breast/breast data files/MYC/rawData", chipType = > "Mapping50K_Hind240") > > > > > > > > > > could anyone enlighten me please? > > > > > > Many thanks > > > > ********************************************************************** > > This email and any files transmitted with it are confidential and > > intended solely for the use of the individual or entity to whom they > > are addressed. If you have received this email in error please notify > > the system manager (it.supp...@cancer.ucl.ac.uk). > > ********************************************************************** > > > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
