[BioC] Lumi methylation analysis errors in lmFit

[Ina Hoeschele]

Hi Jasreet,
   how are you doing the normalization given that you have both Infinium I and II assays?
Thanks, Ina

----- Original Message -----
From: "Jasreet" <jovialj86 at gmail.com>
To: bioconductor at r-project.org
Sent: Thursday, June 2, 2011 11:44:58 AM
Subject: Re: [BioC] Lumi methylation analysis errors in lmFit

Looks like i forgot to paste in traceback . Here is it...

> traceback()
4: stop("incompatible dimensions")
3: lm.fit(design, t(M))
2: lm.series(y$exprs, design = design, ndups = ndups, spacing = spacing,
       weights = weights)
1: lmFit(selDataMatrix, design)

On Thu, Jun 2, 2011 at 10:17 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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