[BioC] Affymetrix design

[Saroj K Mohapatra]

Hi Cintanu:
Something is still not clear. If you only have data from disease (11 
different patients with similar clinical condition), then what are you 
going to compare them with? I think you need at least two groups 
(treatment and control). In this case, you seem to have just one group 
("treatment").

On the other hand, the error message you get is perhaps because limma 
accepts 11 groups in the design matrix but there are no replicates for 
each group.

Best,

Saroj


Sarmah, Chintanu wrote:
> Hi Saroj,
>
> The files have arrived from a lab, and are reported to be from 
> patients (=11 samples) of similar disease type.     
>
> Chintanu
>
> ______________________________
>
>     __________
>     From: Saroj K Mohapatra
>     Sent: Monday, June 15, 2009 3:42:26 AM
>     To: Sarmah, Chintanu
>     Cc: bioconductor at stat.math.ethz.ch
>     <mailto:bioconductor at stat.math.ethz.ch>
>     Subject: Re: [BioC] Affymetrix design
>
>     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
>