[BioC] Lumi methylation analysis errors in lmFit

[Sean Davis]

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
>
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>
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