Hi Sean,

So cant I select just two samples to see the differential expression? Do I
have to do it for all 12 together?

On Thu, Jun 2, 2011 at 1:23 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> Hi, Jasreet.  See below.
>
> On Thu, Jun 2, 2011 at 2:07 PM, Jasreet <jovialj86@gmail.com> wrote:
> > Hi Sean,
> >
> > Here is a brief overview of each object and some steps .. I basically
> want
> > differentially methylated genes between two samples (which I am selecting
> > through sampleType) out of total 12 samples.
> >
> >> mldat
> > MethyLumiM (storageMode: lockedEnvironment)
> > assayData: 485577 features, 12 samples
> >  element names: detection, exprs, methylated, unmethylated
> > protocolData: none
> > phenoData
> >  sampleNames: 3y0eY1 3y0eY2 ... 3y0eXY (12 total)
> >  varLabels: sampleID label
> >  varMetadata: labelDescription
> > featureData
> >  featureNames: cg00000029 cg00000108 ... rs9839873 (485577 total)
> >  fvarLabels: TargetID ProbeID_A ProbeID_B COLOR_CHANNEL
> >  fvarMetadata: labelDescription
> > experimentData: use 'experimentData(object)'
> > Annotation:
> >
> >
> >
> >>presentCount <- detectionCall(mldat)
> >
> >> presentCount[1:3]
> > cg00000029 cg00000108 cg00000109
> >        12         12         12
> >
> >> dim(dataMatrix)
> > [1] 485577     12
> >
> >>selDataMatrix <- dataMatrix[presentCount > 0,]
> >
> >> dim(presentCount)
> > NULL
> >
> >> dim(selDataMatrix)
> > [1] 485574     12
> >
> >>probeList <- rownames(selDataMatrix)
> >
> >> sampleType
> > [1] "3y0eY2" "3y0eY0"
> >
> >>design <- model.matrix(~ factor(sampleType))
>
> If I am not mistaken, sampleType is length 2 while you have 12
> samples?  Not sure how that will work.
>
> Sean
>
> > On Thu, Jun 2, 2011 at 12:13 PM, Sean Davis <sdavis2@mail.nih.gov>
> wrote:
> >
> >> Hi, Jasreet.  It looks like the design matrix and the selDataMatrix
> >> object are not the same dimensions.  You may need to post some code if
> >> you can't find the issue yourself.  In particular, how did you
> >> construct selDataMatrix and "design".
> >>
> >> Sean
> >>
> >>
> >> On Thu, Jun 2, 2011 at 11:17 AM, Jasreet <jovialj86@gmail.com> wrote:
> >> > Hi all
> >> >
> >> > I am new to R and have been using it for Illumina Infinium Methylation
> >> 450 k
> >> > Array analysis using the lumi package.
> >> >
> >> > After normalization, I tried to identify differentially expressed
> genes
> >> > using the example illusrated in the lumi PDF but look like during
> lmFit,
> >> I
> >> > keep getting the same error and hence, I cant move forward.
> >> >
> >> >
> >> > *Error Message : *
> >> >> fit <- lmFit(selDataMatrix, design)
> >> > Error in lm.fit(design, t(M)) : incompatible dimension
> >> > *
> >> > *
> >> > I have also copied sessioninfo and traceback.Any help would be highly
> >> > appreciated.
> >> >
> >> > Thanks
> >> > -jess
> >> > *
> >> >
> >> > Session Info :*
> >> >> sessionInfo()
> >> > R version 2.13.0 (2011-04-13)
> >> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> >> >
> >> > locale:
> >> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> >> >
> >> > attached base packages:
> >> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >> >
> >> > other attached packages:
> >> >  [1] limma_3.8.2
> >> > MASS_7.3-13
> >> IlluminaHumanMethylation450k.db_1.0.7
> >> > org.Hs.eg.db_2.5.0                    RSQLite_0.9-4
> >> >  [6] DBI_0.2-5
> >> > AnnotationDbi_1.14.1                  lumi_2.4.0
> >> > nleqslv_1.8.5                         Biobase_2.12.1
> >> >
> >> > loaded via a namespace (and not attached):
> >> >  [1] affy_1.30.0           affyio_1.20.0         annotate_1.30.0
> >> > grid_2.13.0           hdrcde_2.15           KernSmooth_2.23-5
> >> > lattice_0.19-26       Matrix_0.999375-50
> >> >  [9] methylumi_1.8.0       mgcv_1.7-6            nlme_3.1-101
> >> > preprocessCore_1.14.0 tools_2.13.0          xtable_1.5-6
> >> >
> >> >        [[alternative HTML version deleted]]
> >> >
> >> > _______________________________________________
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> >> > Bioconductor@r-project.org
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >
> >>
> >
> >        [[alternative HTML version deleted]]
> >
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> >
>

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