Dear James,
Sorry, yes;(the other way around) Brian the snail is from the famous UK TV
program as I want a dedicated mail account for Bioconductor (tired of
sorting personal emails), JH is now unsubscribed.

Thanks for the clear answer. Interestingly I ran again at home using the One
class example in the samr documentation, which gives the same output.

      Row   Gene ID Gene Name Score(d)           Numerator(r)
 Denominator(s+s0)   q-value(%)
 [1,] "271" "g270"  "270"     "3.95220187465345" "1.28892719353853"
 "0.326128885724379" "0"
 [2,] "961" "g960"  "960"     "3.58479471552993" "2.33829323731544"
 "0.652280931788244" "0"
 [3,] "647" "g646"  "646"     "3.51526436711204" "2.00153278609765"
 "0.569383288728867" "0"
 [4,] "761" "g760"  "760"     "3.43862390232555" "1.53773350792769"
 "0.447194445105705" "0"
 [5,] "338" "g337"  "337"     "3.06940912129119" "1.85532829874772"
 "0.604457804558568" "0"

But if the numerator is the equivalent of log2(fold change) then it is only
a column name difference. Great. Thanks again,

John

On Tue, Sep 14, 2010 at 7:22 PM, James W. MacDonald
<jmacdon@med.umich.edu>wrote:

> 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$genes.lo)
>> [1] "Row"               "Gene ID"           "Gene Name"
>> "Score(d)"
>> [5] "Numerator(r)"      "Denominator(s+s0)" "q-value(%)"
>>
>> Did I run SAMR in the wrong manner?
>>
>
> I dunno. I assume since you got output that things are at least semi OK.
> You don't give the output of sessionInfo(), so I don't know if you are using
> some old version that doesn't give fold change yet. Anyway, it's irrelevant
> I suppose, because you don't need fold change to be given explicitly.
>
> Note that the numerator of a t-statistic is simply the difference in the
> mean between two groups. In your case (if in fact your case is the same as
> Brian Snail's case), this difference is intrinsic to the ratios you fed into
> samr. Assuming you took logs, what you fed into samr was log2(R/G), which is
> the same as log2(R) - log2(G), e.g., the difference between the red and
> green channel, on the log scale.
>
> The numerator of the resulting t-statistic is the mean of these ratios. So
> depending on what you mean by fold change, you already have it (I prefer to
> work in the log space) or you can exponentiate to get the fold change on the
> natural scale.
>
> Best,
>
> Jim
>
>
>
>
>>
>>
>>
>> On Tue, Sep 14, 2010 at 2:36 PM, James W. MacDonald
>> <jmacdon@med.umich.edu>wrote:
>>
>>  Hi Brian,
>>>
>>>
>>> On 9/14/2010 4:30 AM, brian snail wrote:
>>>
>>>  Hi.
>>>> Below is an outline of the code I am using to analyse two colour array
>>>> data.
>>>> Normal = Cy3
>>>> Case = Cy5
>>>> There are 3 replicates.
>>>>
>>>> Can the fold change be reported back in the siggenes.table? From the
>>>> documentation, it is not obvious how this is done.
>>>>
>>>>
>>> I'm not sure what you are asking here. If I run the example for
>>> samr.compute.siggenes.table, and then look at the colnames for the two
>>> relevant list members I get:
>>>
>>>  colnames(siggenes.table$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
>>>  _______________________________________________
>>> Bioconductor mailing list
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>>>
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>>
>> _______________________________________________
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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
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

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