Hi again, On Fri, Nov 19, 2010 at 10:35 AM, Henrik Bengtsson <henrik.bengts...@gmail.com> wrote: > 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/.
Actually, although that was also an error, the error message reported on is that it cannot locate the annotation data file. Again, see the above two URLs; you need to setup annotationData/chipTypes/Mapping50K_Hind240/ so it contains the correct CDF file etc. You need to download the CDF file from the Affymetrix website, cf. http://aroma-project.org/faq/ /Henrik > >> >> >> >> 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/
