[BioC] expression set object for metaanalysis

[James W. MacDonald]

Hi Peevi,

On 1/14/2011 3:51 PM, Peevi Ijkl wrote:
> hello list
> I know i have been asking the same question over and over again but i just want
> to make sure am clear.

Yes you have been asking the same thing over and over. In addition, you 
have been posting the same question under different subject lines. And 
you have not responded to requests for your sessionInfo() output, even 
after it was explained to you in very nice terms what that meant. And 
you have either not read the posting guide, or have chosen to ignore it.

So let me be clear as well. This is a volunteer mailing list where the 
respondents are choosing to take their time to help answer questions for 
free. In order to get people to take time to read, understand, and then 
diagnose your problem, you need to make it easy for that to happen. This 
is why you were asked for your sessionInfo().

In addition, it is considered bad form to repost the same question over 
and over, using different subject lines. You may think that will 
increase the odds that somebody will see your question, but in fact 
those of us who answer questions see _all_ the questions, and people who 
abuse the system like that will tend to be ignored.

Now the code you post below won't work as written, so you have either 
made some copy-paste errors, or are simply typing what you think you ran 
into this email. This isn't helpful.

What we need is the actual R session, including the output. Since that 
can get very long, you should eliminate all steps that are not necessary 
to show the problem you are having. After you have run the offending 
code, you also have to run sessionInfo() and add that output to the email.

If you have questions about what something like sessionInfo() means, you 
can always type ?sessionInfo at the R prompt to see the help page. By 
trying to figure things out on your own and showing that you have done 
so, people will be more likely to want to help you.

Best,

Jim


> I am loading the CEL files into R using ReadAffy along with the phenodata..then
> I am performing normalization.Now i want to create another expression set object
>
> which I can use for meta-analysis but I am not able to.Any suggestions will be
> helpful.
> thanks
> peevi
>
> pd<- read.AnnotatedDataFrame( "target.txt", header=T, row.names=1, sep=";" )
> pData(pd)
> expression_data<- ReadAffy( filenames = rownames (pData(pd)) )
> expression_data
> rma_expression_data<-rma(expression_data)
> f1<- function( x ) ( IQR(x)>  0.5 )
> ff<- filterfun(f1)
> rma_filtered<- genefilter( rma_expression_data, ff )
> sum(rma_filtered)
> rma_data_selected<- rma_expression_data [ rma_filtered, ]
> dim(rma_expression_data)
> dim(rma_data_selected)
>
> till here I have no errors at all..after this i try the following..
>
> data1<-new("ExpressionSet",exprs=rma_data_selected,phenodata=pData,annotation="hgu133a2")
>
>
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "annotatedDataFrameFrom", for
> signature "ExpressionSet".
>
> please help!
>
>
>
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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