Dear Zhijin: I used R 2.6alpha devel version to generate cdf and probe packages. But when I run GCRMA, I got the following error message: Adjusting for optical effect..Done. Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : NAs are not allowed in subscripted assignments I don't have problem to do GCRMA using my original cdf and probesequence files. I put all of original and updated CDF and probesequence files, and packages which generated by R 2.6 on the following url: http://ci.vbi.vt.edu/yan/newcdf/ehis_index.html Thank you very much for your time. Best yan On Wed, September 12, 2007 4:36 pm, Zhijin Wu wrote: > Hi Yan, > I will need the source file for a probepackage so that I can install the > probepacakge, in order to test out the function compute.affinites for you. > Could you contact the maintainer for the matchprobe package to > solve that problem first? > > Zhijin > Yan Zhang wrote: > >> Dear Dr. Wu: >> There is no NA in my probesequence file. >> I downloaded newest version matchprobes >> package(1.8.1), I got the following error message: >> >> makeProbePackage("ehis1a520285f",version="1.0",species="ehis",maint aine >> r="yanzhang<yzhang at="" vbi.vt.edu="">",build=FALSE, >> >> check=FALSE, force=True) Importing the data. >> Error in rep(NA, max(pm1, mm1, pm2, mm2)) : >> invalid 'times' argument In addition: Warning messages: >> 1: NAs introduced by coercion in: as.integer.default(dat[[2]]) >> 2: NAs introduced by coercion in: as.integer.default(dat[[3]]) >> 3: NAs introduced by coercion in: as.integer.default(dat[[4]]) >> >> >> Using newest version, I even could not generate probe package. >> >> >> I put cdf file and probesequence file at this url: >> >> >> http://ci.vbi.vt.edu/yan/newcdf/ehis_index.html >> >> >> Thank you very much for your time. >> best yan >> >> >> >> Zhijin Wu wrote: >> >> >>> I am not sure what's causing the problem, since we actually allow NAs >>> in the sequences. I wonder if this has anything to do with your >>> trimmed probe package. Can you check first by loading the >>> probepackage, and use >>> >>> myseq <- get("probepackageName") >>> >>> and see how many NAs do you get in tableis.na(myseq$seq))? >>> >>> You may also send me source file of your probepackage. I can't >>> promise to test it immediately but will try my best. >>> >>> >>> yzhang at vbi.vt.edu wrote: >>> >>>> Dear Dr. Wu: >>>> >>>> >>>> Thank you very much for your fast response. The R version is 2.5 >>>> and I am >>>> using bioconductor 2.0. I think may be I did not descripte my >>>> question clearly. My new CDF file is an updated CDF file. Probeset >>>> name changed. Some probe reassign to new probeset, some are deleted. >>>> My new probeequence file is >>>> also a trimmed file compare to old probesequence file. But cel file >>>> doesn't change(this is an customer made affymetrix chip). The >>>> reason why I have the new updated CDF and probesequence file is >>>> because that TIGR reannotation this bacteria genome and correctted a >>>> lot of mistake. I believe that this kind of problem(reannoation >>>> genome and have new CDF and probesequence file) will become more and >>>> more popular in the near future. For using RMA, I don't have problem >>>> to using new CDF file. But, If I want to using GCRMA, I will receive >>>> Error message: >>>> >>>> >>>> Error in compute.affinities(cdfName(object), verbose = verbose) : >>>> NAs are not allowed in subscripted assignments >>>> >>>> >>>> Could you help me to figure out what cause this problem? How could >>>> I >>>> solve it? >>>> >>>> >>>> Best >>>> yan >>>> >>>> >>>> >>>> >>>> >>>> On Fri, September 7, 2007 1:17 pm, Zhijin Wu wrote: >>>> >>>> >>>>> which versions are you using( your affy, gcrma and cdf packages)? >>>>> I >>>>> don't have a problem with the hgu95a or hgu133a platforms. >>>>> yzhang at vbi.vt.edu wrote: >>>>> >>>>> >>>>>> Dear Dr. Zhijin Wu: >>>>>> >>>>>> >>>>>> >>>>>> This is Yan Zhang from VBI. >>>>>> From the retrived message of bioconductor mailing list, >>>>>> https://stat.ethz.ch/pipermail/bioconductor/2005-April/008338.ht >>>>>> ml I noticed that you and James helped Wenqiong Chen to solve >>>>>> the gcrma problem cause by using new CDF and probesequence >>>>>> files. Could you recall how you guys finally solve that problem? >>>>>> >>>>>> My problem is I am trying to use the new CDF and probesequence >>>>>> files to do gcrma normalization for using gcrma function in R. I >>>>>> can use new cdf file to generate new cdf envirment and do RMA. I >>>>>> can also generate probe package and install it without any >>>>>> problem. But when I run gcrma, I got the following error message: >>>>>> >>>>>> >>>>>> >>>>>> Error in compute.affinities(cdfName(object), verbose = verbose) >>>>>> : >>>>>> NAs are not allowed in subscripted assignments >>>>>> >>>>>> >>>>>> >>>>>> If I switch to old CDF and probesequence file, I don't have >>>>>> this problem. >>>>>> >>>>>> For the new sequence file, I did following modification: >>>>>> 1. remove probe type coloumn(if I don't remove it, I could not >>>>>> make probe package) 2. added affymetrix control probe sequence >>>>>> from old probe squence file.(doesn't improve, still get the same >>>>>> error message). >>>>>> >>>>>> >>>>>> I put the commands which I used in error messasge file. I also >>>>>> put new and old cdf, and probesequence files on the web. You >>>>>> could download them from url: >>>>>> http://ci.vbi.vt.edu/yan/newcdf/ehis_index.html >>>>>> >>>>>> >>>>>> >>>>>> Could you help me to figure out this issue? >>>>>> >>>>>> >>>>>> >>>>>> best yan >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> ------------------------------------------- >>>>> Zhijin (Jean) Wu >>>>> Assistant Professor of Biostatistics >>>>> Brown University, Box G-S121 >>>>> Providence, RI 02912 >>>>> >>>>> >>>>> >>>>> Tel: 401 863 1230 >>>>> Fax: 401 863 9182 >>>>> http://stat.brown.edu/~zwu >>>>> >>>>> >>>>> >>>> >>>> >>> >>> > > > -- > ------------------------------------------- > Zhijin (Jean) Wu > Assistant Professor of Biostatistics > Brown University, Box G-S121 > Providence, RI 02912 > > > Tel: 401 863 1230 > Fax: 401 863 9182 > http://stat.brown.edu/~zwu > >