Thanks! Ligia. I will make the change. Probably, we will just remove the sub-sampling step by default. Have a nice weekend, Pan On 12/14/07 3:56 PM, "ligia at ebi.ac.uk" <ligia at="" ebi.ac.uk=""> wrote: > Hi Pan, > > Thanks for your email. > The problem I reported is not due to the downsampling step controlled via > "nSupport" parameter, but with a subsequent step in "vst" where if the > number of selected probes with high variance (indSel) is above 5000, then > only a random subset (5000) of these probes is used (the steps I mentioned > in my last email) to fit the linear model between variance and mean of > probe beads. Couldn't this value (5000) be just another parameter to > "vst"? > > Thanks for your help, > Ligia > > > >> Hi Ligia, >> >> Thanks for your report. >> Yes, we use down-sampling to speed up the parameter estimation. If you >> want >> to use all the data points, you can set the parameter "nSupport" of vst >> function as the length of the vector. I will add this to the vignette or >> help file. Thanks! >> >> >> Pan >> >> >> On 12/14/07 5:18 AM, "ligia at ebi.ac.uk" <ligia at="" ebi.ac.uk=""> wrote: >> >>> Dear Pan Du, >>> >>>> From what I understand when looking at "vst", the random subsampling >>>> that >>> affects my data occurs at step 4 below: >>> >>> 1 if (c3 != 0) { >>> 2 selInd <- selInd & (std^2 > c3) >>> 3 dd <- data.frame(y = sqrt(std[selInd]^2 - c3), x1 = >>> u[selInd]) >>> 4 if (nrow(dd) > 5000 dd <- dd[sample(1:nrow(dd), 5000), ] >>> 5 lmm <- lm(y ~ x1, dd) >>> 6 c1 <- lmm$coef[2] >>> 7 c2 <- lmm$coef[1] >>> 8 } >>> >>> because my "dd" matrix has around 5500 rows. Maybe it would be nice to >>> have the option to turn this off, or add the option to provide the max >>> value allowed for nrow(dd)... >>> >>> Cheers, >>> L?gia >>> >>> >>>> Dear Ligia >>>> >>>> I believe this is because they random subsample the data to "speed >>>> processing", see the man page and the nSupport parameter. >>>> >>>> I cc Pan Du with the suggestion to make the explanation of this in the >>>> man page more clear. Is there an option to switch off the random >>>> subsampling? >>>> >>>> Best wishes >>>> Wolfgang >>>> >>>> >>>> >>>> ligia at ebi.ac.uk ha scritto: >>>>> Hi Wolfgang, >>>>> >>>>> I noticed a peculiar behaviour in lumi package: when I apply the >>>>> variance >>>>> stabilizing transformation, >>>>> it gives slightly different results each time I run the method. See >>>>> below >>>>> for a subset of the data: >>>>> >>>>> >>>>>> load("dat.rda") >>>>>> library("lumi") >>>>> >>>>>> x1 <- lumiT(dat, method="vst", ifPlot=!TRUE) >>>>> 2007-12-13 10:56:35 , processing array 1 >>>>> 2007-12-13 10:56:35 , processing array 2 >>>>> 2007-12-13 10:56:35 , processing array 3 >>>>> 2007-12-13 10:56:35 , processing array 4 >>>>> >>>>>> x2 <- lumiT(dat, method="vst", ifPlot=!TRUE) >>>>> 2007-12-13 10:56:36 , processing array 1 >>>>> 2007-12-13 10:56:36 , processing array 2 >>>>> 2007-12-13 10:56:36 , processing array 3 >>>>> 2007-12-13 10:56:37 , processing array 4 >>>>> >>>>> >>>>>> table(exprs(x1)==exprs(x2)) >>>>> >>>>> FALSE TRUE >>>>> 88705 3 >>>>> >>>>>> range(exprs(x1)-exprs(x2)) >>>>> [1] -0.05682931 0.03592777 >>>>> >>>>>> sessionInfo() >>>>> R version 2.7.0 Under development (unstable) (2007-11-29 r43558) >>>>> i686-pc-linux-gnu >>>>> >>>>> locale: >>>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE =en_US.UTF >>>>> -8 >>>>> ;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_N >>>>> AM >>>>> E=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID ENTIFICATI >>>>> ON >>>>> =C >>>>> >>>>> attached base packages: >>>>> [1] tools stats graphics grDevices utils datasets >>>>> methods >>>>> [8] base >>>>> >>>>> other attached packages: >>>>> [1] lumi_1.5.10 annotate_1.15.6 AnnotationDbi_1.1.6 >>>>> [4] RSQLite_0.6-0 DBI_0.2-3 mgcv_1.3-29 >>>>> [7] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.7 >>>>> [10] Biobase_1.17.6 >>>>> >>>>> Cheers, >>>>> Ligia >>>> >>>> >>>> -- >>>> >>>> Best wishes >>>> Wolfgang >>>> >>>> ------------------------------------------------------------------ >>>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>>> >>> >>> >> >> >> --------------------------------------------------- >> Pan Du, PhD >> Research Assistant Professor >> Robert H. Lurie Comprehensive Cancer Center >> Northwestern University >> 676 ST Clair St., #1200 >> Chicago, IL 60611 >> Office (312)695-4781 >> dupan at northwestern.edu >> --------------------------------------------------- >> >> >> >> >> > >