To test other possibilities, I modified the following function theta <- extractMatrix(ces, returnUgcMap=TRUE) to theta <- extractMatrix(ces, returnRefcMap=TRUE) It gave the same result.
On Aug 14, 11:57 am, tea <ywcu...@gmail.com> wrote: > Hi Mark, > > The following are the outputs:> cdf<- getCdf(cs) > > print(cdf) > > AffymetrixCdfFile: > Path: annotationData/chipTypes/HG-U133A > Filename: HG-U133A.cdf > Filesize: 41.16MB > Chip type: HG-U133A > RAM: 0.00MB > File format: v3 (text; ASCII) > Dimension: 712x712 > Number of cells: 506944 > Number of units: 17599 > Cells per unit: 28.81 > Number of QC units: 10> print(getMonoCell(cdf)) > > AffymetrixCdfFile: > Path: annotationData/chipTypes/HG-U133A > Filename: HG-U133A,monocell.CDF > Filesize: 3.11MB > Chip type: HG-U133A,monocell > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 147x146 > Number of cells: 21462 > Number of units: 17599 > Cells per unit: 1.22 > Number of QC units: 10> print(getCdf(ces)) > > AffymetrixCdfFile: > Path: annotationData/chipTypes/HG-U133A > Filename: HG-U133A,monocell.CDF > Filesize: 3.11MB > Chip type: HG-U133A,monocell > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 147x146 > Number of cells: 21462 > Number of units: 17599 > Cells per unit: 1.22 > Number of QC units: 10 > > On Aug 14, 1:51 am, Mark Robinson <mrobin...@wehi.edu.au> wrote: > > > Hi Yiwen. > > > Can you check a couple quick things for me? > > > What does the output of these give: > > > cdf <- getCdf(cs) > > > print(cdf) > > > print(getMonoCell(cdf)) > > > print(getCdf(ces)) > > > Cheers, > > Mark > > > On 14-Aug-09, at 1:44 PM, tea wrote: > > > > Hi, > > > > I used the script in the following page: > > >http://groups.google.com/group/aroma-affymetrix/web/redundancy-tests > > > to process a dataset of 189 arrays using Human custom refseq CDF > > > version 10, HGU133A_Hs_REFSEQ > > > After I finished > > > fit(plm, verbose=verbose) > > > I got the following message: > > > " > > > Total time for all units across all 189 arrays: 532.37s == 8.87min > > > Total time per unit across all 189 arrays: 0.04s/unit > > > Total time per unit and array: 0.235ms/unit & array > > > Total time for one array (17599 units): 0.07min = 0.00h > > > " > > > When I finished up to the code > > > ces <- getChipEffectSet(plm); > > > theta <- extractMatrix(ces, returnUgcMap=TRUE); > > > theta <- log2(theta); > > > ugcMap <- attr(theta, "unitGroupCellMap"); > > > rownames(theta) <- getUnitNames(getCdf(ces), ugcMap[,"unit"] > > > and type > > > > dim(theta) > > > I found that he total number of probesets is only 11979. > > > "11979 189" > > > > If I used affy(rma) and tested on a small number of CEL file from the > > > same dataset, the total number of probesets is 17599. > > > > From the custom cdf document the total number of probeset of this cdf > > > is 17531, so with the "AFFX" probes(68), > > > the total number should be 17599. I was wondering what parameter > > > should be used to get right number of probesets from cdf file for > > > refseq, entrezg, ug respectively > > > > Thank you very much. > > > > -Yiwen Chen > > > ------------------------------ > > Mark Robinson, PhD (Melb) > > Epigenetics Laboratory, Garvan > > Bioinformatics Division, WEHI > > e: m.robin...@garvan.org.au > > e: mrobin...@wehi.edu.au > > p: +61 (0)3 9345 2628 > > f: +61 (0)3 9347 0852 > > ------------------------------ --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
