[BioC] Affymetrix design

[Saroj K Mohapatra]

Hi Chintanu:

Are there 11 arrays for 11 treatments without any biological replication?

Saroj

Sarmah, Chintanu wrote:
> Hi All,
> I’m trying to find the differentially expressed genes in a set of treatment samples (i.e., no ‘control’ samples) of Affymetrix platform.
> While attempting the linear models explained in Limma, I have tried the following but am unsure whether what I am doing is correct and how to correct the error. I also wonder if there is some other way of doing it. Your pointers would be very helpful.
> Thank you.
> Cheers,
> Chintanu
> = = ==  = =  = =  = = = = = =   ==  = = =
> groups<-c("T1","T2","T3","T4","T5","T6","T7","T8","T9","T10", "T11")
> groups<-as.factor(groups)
> design<-model.matrix(~groups)
>
> myRMA <- justRMA()
> fit <- lmFit(myRMA, design)
>  fit <- eBayes(fit)
> Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) :
>   No residual degrees of freedom in linear model fits
>
>
>   
>> sessionInfo()
>>     
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] limma_2.18.0         hgu133plus2cdf_2.4.0 KEGG.db_2.2.11       GO.db_2.2.11         RSQLite_0.7-1        DBI_0.2-4            AnnotationDbi_1.6.0
>  [8] affyQCReport_1.22.0  lattice_0.17-25      RColorBrewer_1.0-2   affyPLM_1.20.0       preprocessCore_1.6.0 xtable_1.5-5         simpleaffy_2.20.0
> [15] gcrma_2.16.0         Biostrings_2.12.1    IRanges_1.2.1        genefilter_1.24.0    affy_1.22.0          Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0   annaffy_1.16.0  annotate_1.22.0 grid_2.9.0      splines_2.9.0   survival_2.35-4 tools_2.9.0
>
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>
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