Hi.
On Tue, Jul 21, 2009 at 9:23 PM, Stellaw Chao<stellaw.c...@gmail.com> wrote:
>
> Dear aroma.affymetrix developers,
> I am a little bit confused while using ur package aroma.affymetrix to
> process my dataset.
> The following is my code——
>
> setwd("C:/Array Files_CP2Bonly")
> library("aroma.affymetrix")
> cs <- AffymetrixCelSet$fromName("HapMap100K-bioc2007",
> chipType="HG-U133_Plus_2")
> qn <- QuantileNormalization(cs)
> csQN <- process(qn, verbose=TRUE)
> plm<-RmaCnPlm(csQN,combineAlleles=TRUE, mergeStrands=TRUE)
> fit(plm, verbose=TRUE)
>
> after the RmaCnPlm procedure, a set of new CEL Files(e.g.
> "Mao101C075B,chipEffects" for an original CEL file "Mao101C075B") are
> generated, yet I am not very clearly about the meaning of these new
> Files, as their sizes are much smaller than the original ones (590KB
> vs.13,225KB)They hold the summarized signals (in contrast to one per probe). You should access the signals in those files using extractMatrix(), extractTheta(), or extractDataFrame() which are available for single arrays (files) as well as sets of arrays (files), e.g. ces <- getChipEffectSet(plm); ce <- getFile(ces, 2); theta <- extractTheta(ce, units=1001:1012); theta <- extractTheta(ces, units=1001:1012); data <- extractDataFrame(ce, units=1001:1012, addNames=TRUE); data <- extractDataFrame(ces, units=1001:1012, addNames=TRUE); See also vignette: http://groups.google.com/group/aroma-affymetrix/web/calculating-raw-total-copy-numbers-manually Unless you're a developer, consider those *,chipEffects.CEL files to be internal files of aroma.affymetrix. The details is that they only hold one cell ("probe") signal per unit group ("probeset"), which is also why they are smaller. They are read using the corresponding "monocell" CDF created automatically, e.g. HG-U133_Plus_2,monocell.cdf. See print(getCdf(ces)). /Henrik > > Much Thanks for your help! Look forward to your reply! > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
