I have realised that the annotations I have been using are incorrect so the information I mentioned regarding RT1-C113 is irrelavant. However, I would still like to know how to (if possible) change the options for probe skipping. cheers, Sebastien
Sebastien Gerega wrote: > Thanks for the insight Mark. I have included the gene symbols for the > 183 probes with greater than 100 cells per unit. It turns out 147 of > them are for the same gene RT1-C113 This gene has been the following > summary at NCBI > (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=24151) > > : > > Summary > DISCONTINUED: This record has been withdrawn by RGD > > What is the meaning of all this? > > And is there a way to change the options for aroma so that the probes > with greater than 100 cells per unit are skipped? Or would I have to > remove them manually? > thanks again, > Sebastien > > > > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "C1r" > "Mphosph10" > "Ruvbl1" > "Tmem34" > "Pim2" > "RGD1561513" > "Fstl1" > "Areg" > "RT1-C113" > "Id3" > "RT1-C113" > "RGD1308106" > "Cops5" > "Vil1" > "Sppl3" > "Mobkl1a" > "Zfp143" > "RGD1565370" > "Qprt" > "Rangap1" > "Pde6d" > "Tmem199" > "Alcam" > "RGD1311493" > "Cpa6" > "RGD1624210" > "Cops5" > "RT1-C113" > "Pygo2" > "RGD1562372" > "Rb1cc1" > "Kcne3" > "Porcn" > "Rras" > "Cuta" > "Zfp313" > "Olr1333-ps" > "RGD1562284" > "Epb4.1l5" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > "RT1-C113" > > > > > Mark Robinson wrote: >> Hi Sebastien. >> >> Interesting observation, I hadn't noticed that. >> >> Since the major difference is in the fitting stage, my guess would >> be that there are just more larger units (although less total units) >> in the RaGene CDF. This is certainly true for say, the number of >> probesets with more than 100 probes: >> >> >> cdf1 <- AffymetrixCdfFile$fromChipType("RaGene-1_0-st-v1",tags="r3") >> cdf2 <- AffymetrixCdfFile$fromChipType("HuGene-1_0-st-v1",tags="r3") >> cpu1 <- nbrOfCellsPerUnit(cdf1) >> cpu2 <- nbrOfCellsPerUnit(cdf2) >> >> > sum(cpu1 > 100) >> [1] 183 >> > sum(cpu2 > 100) >> [1] 70 >> >> I haven't looked in close detail, but it may be worth removing some >> of the large probesets in the interest of speed. Sometimes these >> are just controls anyways. aroma.affymetrix already does this by >> default for the super large probesets (it jumps to median polish >> instead of a robust linear model). >> >> > options()$aroma.affymetrix.settings$models$RmaPlm >> $medianPolishThreshold >> [1] 500 6 >> >> $skipThreshold >> [1] 5000 1 >> >> >> Hope that helps. >> Mark >> >> >> >> On 27/02/2009, at 5:57 PM, Sebastien Gerega wrote: >> >> >>> Hi, >>> I have been playing around with the Aroma package and using sample >>> data >>> from the Affymetrix site. I've noticed that normalising ragene10st >>> arrays takes about 10 times longer than it does for hugene10st. For >>> example: >>> ragene10st: >>> >>> Total time for complete data set: 20.31min = 0.34h >>> Fraction of time spent on different tasks: Fitting: 96.5%, Reading: >>> 0.9%, Writing: 2.6% (of which 60.78% is for encoding/writing >>> chip-effects), Explicit garbage collection: 0.0% >>> >>> >>> hugene10st: >>> Total time for complete data set: 2.38min = 0.04h >>> Fraction of time spent on different tasks: Fitting: 69.6%, Reading: >>> 6.5%, Writing: 23.5% (of which 61.68% is for encoding/writing >>> chip-effects), Explicit garbage collection: 0.4 >>> >>> Both analyses are being run with 6 cel files. Is this expected and >>> if so >>> what is the reason for the difference? >>> thanks, >>> Sebastien >>> >>> >>> >> >> ------------------------------ >> Mark Robinson >> Epigenetics Laboratory, Garvan >> Bioinformatics Division, WEHI >> e: [email protected] >> e: [email protected] >> 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 [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
