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

[James W. MacDonald]

Hmm. Did Brian Snail morph into Johnny H?

On 9/14/2010 11:01 AM, Johnny H wrote:
> Hi James
> thanks for the answer, :-) Perl is not so bad

No, Perl is fine. I wasn't bashing. Just noting that R doesn't use 
semicolons for line delimiters, so adding them is IMO ugly.

>
> With my data, I get this....
>
> colnames(siggenes.table$genes.lo)
> [1] "Row"               "Gene ID"           "Gene Name"
> "Score(d)"
> [5] "Numerator(r)"      "Denominator(s+s0)" "q-value(%)"
>
> Did I run SAMR in the wrong manner?

I dunno. I assume since you got output that things are at least semi OK. 
You don't give the output of sessionInfo(), so I don't know if you are 
using some old version that doesn't give fold change yet. Anyway, it's 
irrelevant I suppose, because you don't need fold change to be given 
explicitly.

Note that the numerator of a t-statistic is simply the difference in the 
mean between two groups. In your case (if in fact your case is the same 
as Brian Snail's case), this difference is intrinsic to the ratios you 
fed into samr. Assuming you took logs, what you fed into samr was 
log2(R/G), which is the same as log2(R) - log2(G), e.g., the difference 
between the red and green channel, on the log scale.

The numerator of the resulting t-statistic is the mean of these ratios. 
So depending on what you mean by fold change, you already have it (I 
prefer to work in the log space) or you can exponentiate to get the fold 
change on the natural scale.

Best,

Jim


>
>
>
>
> On Tue, Sep 14, 2010 at 2:36 PM, James W. MacDonald
> <jmacdon at med.umich.edu>wrote:
>
>> 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
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be
>> used for urgent or sensitive issues
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>
> 	[[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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues