To whom it may concern, i am very new to BioConductor and have a seemingly basic question. How does one use the 7 different normalization techniques with affy data that is not in a CEL or AFFYBATCH format. Essentially I have Avg.Diff. values of several U133A chips and would like to vis. and normal. using most of the tools found in your affy package. The data is matrix form (text tab-delim. table) with probe names and Avg.Dif values for several samples. I know this isn't ideal but i still wanted to take advantage of the strengths of you package. any help would be greatly appreciated!! David Rickman project leader Ligue Nationale Contre le Cancer France

On Tue, May 06, 2003 at 06:44:34PM +0200, David Rickman wrote: > To whom it may concern, > > i am very new to BioConductor and have a seemingly basic question. How > does one use the 7 different normalization techniques with affy data > that is not in a CEL or AFFYBATCH format. Essentially I have Avg.Diff. > values of several U133A chips and would like to vis. and normal. using > most of the tools found in your affy package. The data is matrix form > (text tab-delim. table) with probe names and Avg.Dif values for several > samples. I know this isn't ideal but i still wanted to take advantage > of the strengths of you package. > > any help would be greatly appreciated!! > > David Rickman > project leader > Ligue Nationale Contre le Cancer > France > Each normalization method working on AffyBatch objects is a wrapper around a another function dealing with matrices (to facilitate the port to other classes (like marray*)) or for cases like yours. Try the vignette about 'custom processing methods' for the naming convention and refer to the individula normalizationmethods help pages. For the visualization you may have to work the things by yourself... Hopin' it helps, L. -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent

Hi, I have been wondering about how to do quantile normalization of affy data for which probe-level data is not available. I found an answer in the mailing list archive (see below) but I'm afraid I can't find the vignette referred to nor can I find any information about whatever function is wrapped by normalize.quantiles. Can someone please give me more specifics about where to look for help? Basically I would like to know how (and if!) I can do quantile normalization of data which is stored e.g. as an R matrix not an AffyBatch object. I appreciate any help - thanks! Matthew ---------------------------------------------------------------------- Matthew Hobbs Garvan Institute of Medical Research 384 Victoria St Ph : (02) 9295 8327 Darlinghurst http://www.garvan.org.au email: m.hobbs@garvan.org.au ---------------------------------------------------------------------- On Tue, May 06, 2003 at 06:44:34PM +0200, David Rickman wrote: > To whom it may concern, > > i am very new to BioConductor and have a seemingly basic question. How > does one use the 7 different normalization techniques with affy data > that is not in a CEL or AFFYBATCH format. Essentially I have Avg.Diff. > values of several U133A chips and would like to vis. and normal. using > most of the tools found in your affy package. The data is matrix form > (text tab-delim. table) with probe names and Avg.Dif values for several -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent * Previous message: [BioC] affy normalization * Next message: [BioC] limma missing files * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the Bioconductor mailing list -- > samples. I know this isn't ideal but i still wanted to take advantage > of the strengths of you package. > > any help would be greatly appreciated!! > > David Rickman > project leader > Ligue Nationale Contre le Cancer > France > Each normalization method working on AffyBatch objects is a wrapper around a another function dealing with matrices (to facilitate the port to other classes (like marray*)) or for cases like yours. Try the vignette about 'custom processing methods' for the naming convention and refer to the individula normalizationmethods help pages. For the visualization you may have to work the things by yourself... Hopin' it helps, L.

Whoops! I asked a dumb question. I see now normalize.quantiles can use as an argument a matrix instead of an AffyBatch object. Sorry about the unneccessary posting. Hi, I have been wondering about how to do quantile normalization of affy data for which probe-level data is not available. I found an answer in the mailing list archive (see below) but I'm afraid I can't find the vignette referred to nor can I find any information about whatever function is wrapped by normalize.quantiles. Can someone please give me more specifics about where to look for help? Basically I would like to know how (and if!) I can do quantile normalization of data which is stored e.g. as an R matrix not an AffyBatch object. I appreciate any help - thanks! Matthew ---------------------------------------------------------------------- Matthew Hobbs Garvan Institute of Medical Research 384 Victoria St Ph : (02) 9295 8327 Darlinghurst http://www.garvan.org.au email: m.hobbs@garvan.org.au