[BioC] Lumi methylation analysis errors in lmFit

[Sean Davis]

Hi, Jasreet.  See below.

On Thu, Jun 2, 2011 at 2:07 PM, Jasreet <jovialj86 at 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 at 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 at 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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>>
>
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>
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