[BioC] How is fold change reported in the samr output?

[James W. MacDonald]

Hi Brian,

On 9/14/2010 4:30 AM, brian snail wrote:
> Hi.
> Below is an outline of the code I am using to analyse two colour array data.
> Normal = Cy3
> Case = Cy5
> There are 3 replicates.
>
> Can the fold change be reported back in the siggenes.table? From the
> documentation, it is not obvious how this is done.

I'm not sure what you are asking here. If I run the example for 
samr.compute.siggenes.table, and then look at the colnames for the two 
relevant list members I get:

 > colnames(siggenes.table$genes.lo)
[1] "Row"               "Gene ID"           "Gene Name"
[4] "Score(d)"          "Numerator(r)"      "Denominator(s+s0)"
[7] "Fold Change"       "q-value(%)"
 > colnames(siggenes.table$genes.up)
[1] "Row"               "Gene ID"           "Gene Name"
[4] "Score(d)"          "Numerator(r)"      "Denominator(s+s0)"
[7] "Fold Change"       "q-value(%)"

But maybe I misunderstand your question?

>
> Thank you for any help.
>
>
>
>
>
> # Code for Two colour data normalised with maNorm. ########
>
> data.normalised<- (two colour array matrix of data);
>
> # Make column names 1, 2 and 3
> colnames(data.normalised)<- seq(1:3);

Ugh. This isn't Perl, or god forbid, SAS. Although the R interpreter is 
happy to strip off these trailing semicolons, they are not necessary, 
and IMO really ugly.

Best,

Jim


>
> # Make the row names gene names
> rownames(data.normalised)<- gene_names;
>
> library(impute);
> # Replace nas with numbers
> imputed<-impute.knn(data.normalised,k=3);
>
> # Take the raw data from impute object
> x<-imputed$data;
>
> # One class, so a list of 1's
> y<-c(rep(1,3));
>
> # Prepare the samr data
> data.sam<- list(x=x, y=y, genenames=rownames(data.normalised),
> geneid=gene_names,logged2=T);
>
> library(samr);
>
> # Do the one class SAMR analysis
> samr.obj<- samr(data.sam,resp.type="One class",nperms=100);
>
> # Set up a delta value
> delta=0.4
>
> # Compute the delta table
> delta.table<- samr.compute.delta.table(samr.obj)
>
> # Collect the significant genes into a table
> siggenes.table<-samr.compute.siggenes.table(samr.obj,delta, data.sam,
> delta.table);
>
> 	[[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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