[aroma.affymetrix] Re: Controls and 100k questions

Hi, On Tue, Dec 2, 2008 at 9:46 AM, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > Hi Henrik! > > I´m processing a analysis of 27 tumors of cervical cancer using 100k > and I´m wondering the following: > > Should I include in the analysis chips with patients without cancer? I > mean "controls"

[aroma.affymetrix] Re: extractRawCopyNumbers question

Hi. On Tue, Dec 2, 2008 at 2:05 PM, Qicheng Ma <[EMAIL PROTECTED]> wrote: > Hi Henrik, > > I followed your instruction of total copy number analysis for 500k: > > In the last few step, we need to run extractRawCopyNumbers, however, > there is no > documents for this function: > ?extractRa

[aroma.affymetrix] Batch Normalization

Hi I have already normalized a set of Affymetrix SNP 6.0 CEL files. The following steps are used AllelicCrosstalkCalibration() AvgCnPlm( ,mergeStrands = TRUE, combineAlleles=TRUE) getChipEffect() FragmentLengthNormalization() IF I need to add few more CEL Files to this study, do I have to reno

[aroma.affymetrix] Re: FIRMA score

Hi Sabrina. Indeed, you'll want to set 'mergeGroups=TRUE' for the probe level model (ExonRmaPlm object) that you send to 'FirmaModel' ... - http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis says: ... plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) print(plmTr)

[aroma.affymetrix] extractRawCopyNumbers question

Hi Henrik, I followed your instruction of total copy number analysis for 500k: In the last few step, we need to run extractRawCopyNumbers, however, there is no documents for this function: ?extractRawCopyNumbers() Non-documented objects package:aroma.core R Documentation Non-d

Re: annotationData over network using Windows Shortcuts *.lnk (Was: Re: [aroma.affymetrix] Re: How do you analyze Gene ST Data?)

Hi, thanks. Almost there. Unfortunately, you left out the one answer I was most interest in; see below. On Tue, Dec 2, 2008 at 12:34 PM, pwhiteusa <[EMAIL PROTECTED]> wrote: > > Hi Henrik, > > The results are interspersed below: > > On Nov 26, 4:27 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wr

Re: annotationData over network using Windows Shortcuts *.lnk (Was: Re: [aroma.affymetrix] Re: How do you analyze Gene ST Data?)

Hi Henrik, The results are interspersed below: On Nov 26, 4:27 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote: > Hi, > > so this is a bit confusing.  I've been trying to reproduce it myself > over a local Windows network, but I cannot.  I did however locate a > potential problem where R incorr

[aroma.affymetrix] Estimated time left: 36844.5min

Hi, I'm trying to analyze 973 SNP6.0 arrays with aroma.affymetrix. The early steps of the analysis went fine, but the probe level summarization step takes a huge amount of time, as you can see in the short log I show below. Here is the command I used: fit(plm, verbose=verbose, ram=10) The machin

Re: Reproducing RMA with Gene ST data (Was: Re: [aroma.affymetrix] Re: How do you analyze Gene ST Data?)

Hi All, Here is the exact code I used to analyze Gene ST data for an experiment performed with the MoGene-1_0-st-v1 array. AROMA.AFFYMETRIX library(aroma.affymetrix) cdf <- AffymetrixCdfFile$fromChipType("MoGene-1_0-st-v1",tags="r3") prefixName <- "Pierson" cs <- AffymetrixCelSet$byName(prefixN

[aroma.affymetrix] Re: Error with chromosomeExplorer

Hi, On Tue, Dec 2, 2008 at 8:06 AM, mortiz <[EMAIL PROTECTED]> wrote: > > hi everyone, > > im trying to proccess chromosomeExplorer and i get this error: > > >> ce <- ChromosomeExplorer(cbs) >> process(ce, verbose=verbose) > ERROR caught in onFit.CopyNumberSegmentationModel(): > unable to start

[aroma.affymetrix] Re: Discussion on affymetrix-defined-transcript-clusters

Here's the reply from Affymetrix Tech Support: *** Hello Dr Fass- There is only a minor difference between the v1 and the v2 library files and it has to do with the manufacturing controls on the array. There is no difference with the probes interrogating t

[aroma.affymetrix] FIRMA score

Hi, all: I just started learning to use firma analysis. My impression from previous discussions of other users is that we should only use plm with mergeGroup=True, is that correct? Another question is : Is unitName same as gene uid in NCBI database? how can I map groupName to EXON name from NCBI?

[aroma.affymetrix] Controls and 100k questions

Hi Henrik! I´m processing a analysis of 27 tumors of cervical cancer using 100k and I´m wondering the following: Should I include in the analysis chips with patients without cancer? I mean "controls" - Should I change something since I don´t have a Y chromosome? Since I only have women in my s

[aroma.affymetrix] Error with chromosomeExplorer

hi everyone, im trying to proccess chromosomeExplorer and i get this error: > ce <- ChromosomeExplorer(cbs) > process(ce, verbose=verbose) ERROR caught in onFit.CopyNumberSegmentationModel(): I get some plots done and others not... > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-min

[aroma.affymetrix] Re: Batch normalization

Hi Henrik What I am doing is the following AllelicCrosstalkCalibration FragmentLengthNormalization This is on a set of affy SNP 6.0 CEL files. I have to add few more CEL files to the dataset. Do I have to renormalize all of thme once more. Thanks Joshy On Nov 25, 2:22 pm, "Henrik Bengtsson" <