[R] limma function problem

[Martin Morgan]

On 02/25/2011 04:26 AM, Sukhbir Rattan wrote:
> Hi,
> 
> I have two data set of normalized Affymetrix CEL files, wild type vs Control
> type.(each set have further three replicates).
> 
> 
>> wild.fish
> AffyBatch object
> size of arrays=712x712 features (10 kb)
> cdf=Zebrafish (15617 affyids)
> number of samples=3
> number of genes=15617
> annotation=zebrafish
> notes=
>> Dicer.fish
> AffyBatch object
> size of arrays=712x712 features (10 kb)
> cdf=Zebrafish (15617 affyids)
> number of samples=3
> number of genes=15617
> annotation=zebrafish
> notes=
> 
> Now, I have to combine these two S4 objects and use lmFit function of Limma
> package.I am able to combine the two S4 objects using merge function.
> 
> 
>> merge.fish <-merge(wild.fish,Dicer.fish)
>> merge.fish
> AffyBatch object
> size of arrays=712x712 features (17833 kb)
> cdf=Zebrafish (15617 affyids)
> number of samples=6
> number of genes=15617
> annotation=zebrafish
> notes=Merge from two AffyBatches with notes: 1)  , and 2)
> 
>> design
>              Wild Mz_Dicer
> GSM95623.CEL    1        0
> GSM95624.CEL    1        0
> GSM95625.CEL    1        0
> GSM95617.CEL    0        1
> GSM95618.CEL    0        1
> GSM95619.CEL    0        1
> 
> 
>> fit <-lmFit(merge.fish, design)
> Error in as.vector(data) :
>   no method for coercing this S4 class to a vector
> 
>> mode(merge.fish)
> [1] "S4"
> 
> 
> So, how to troubleshoot this problem?

Hi Sukhbir -- this is a Bioconductor package, so please ask on that list.

http://bioconductor.org/help/mailing-list/

However, you'll want to review basic microarray analysis work flows in
R, either on the Bioconductor web site

http://bioconductor.org/help/workflows/oligo-arrays/

or other resources, such as the vignette that comes with affy or limma.
What you have is 'raw' data; you want to 'pre-process' it, e.g., by the
RMA algorithm, prior to assessing differential expression. A more
typical work flow might go directly from your 6 CEL files to an
'ExpressionSet' object using RMA normalization, via the single function
call just.rma from the affy package; no need to ReadAffy and merge.

Hope that helps.

Martin

> 
> 
> Regards,
> Sukhbir Singh Rattan.....
> 
> 	[[alternative HTML version deleted]]
> 
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