Question: Question on Affxparser (createCel)
0
11.1 years ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:
As you may recall, I am trying to create CEL files from an AffyBatch object (after having my original CEL files be corrected by Harshlight). http://article.gmane.org/gmane.science.biology.informatics.conductor/1 87 57 Since my R-skills are very basic, for this I mainly rely on understanding examples available in vignettes or BioC mailing list... As suggested, I would like to use the 'createCel' and 'updateCel' commands from Affxparser. However, there is one thing in the 'createCel' help page i don't understand, which has to do with the type of the CEL file (binary,ASCII): why should the version of the original input CEL files (that are used as template to create the new, updated files) explicity be of version 3 (type = ASCII?)? After reading the help page I understand that the OUTPUT cannot be anything else than v4 (type = binary), but what about the input? See below. Thanks, Guido <copy paste="" from="" help="" page="" 'createcel'=""> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Read the CEL header # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hdr <- readCelHeader(file) stopifnot(hdr$version == 3) ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> email: guido.hooiveld@wur.nl [[alternative HTML version deleted]] affxparser • 394 views ADD COMMENTlink modified 11.1 years ago by Henrik Bengtsson2.4k • written 11.1 years ago by Guido Hooiveld2.5k Answer: Question on Affxparser (createCel) 0 11.1 years ago by United States Henrik Bengtsson2.4k wrote: Hi. On Tue, Aug 5, 2008 at 6:46 AM, Hooiveld, Guido <guido.hooiveld at="" wur.nl=""> wrote: > > As you may recall, I am trying to create CEL files from an AffyBatch > object (after having my original CEL files be corrected by Harshlight). > http://article.gmane.org/gmane.science.biology.informatics.conductor /187 > 57 > > Since my R-skills are very basic, for this I mainly rely on > understanding examples available in vignettes or BioC mailing list... > As suggested, I would like to use the 'createCel' and 'updateCel' > commands from Affxparser. > > However, there is one thing in the 'createCel' help page i don't > understand, which has to do with the type of the CEL file > (binary,ASCII): > why should the version of the original input CEL files (that are used as > template to create the new, updated files) explicity be of version 3 > (type = ASCII?)? > > After reading the help page I understand that the OUTPUT cannot be > anything else than v4 (type = binary), but what about the input? See > below. The template CEL header (argument 'header') can be of any version, i.e. v3 (ASCII), v4 (binary;XDA), or v1 (binary;Calvin). I have clarified this in the help(createCel) in the next release/the developers version. The easiest is to "reuse" one you get from readCelHeader() of an existing CEL file The stopifnot(hdr$version == 3) expression of example(createCel) is just to assert that the generic code above found an ASCII file. It is just to catch stupid mistakes when R CMD check runs. In the next release/the developers version, I have added a comment explaining this. Hope this helps Cheers Henrik > > Thanks, > Guido > > <copy paste="" from="" help="" page="" 'createcel'=""> > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Read the CEL header > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > hdr <- readCelHeader(file) > stopifnot(hdr\$version == 3) > > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > email: guido.hooiveld at wur.nl > > > [[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 >