[BioC] How to save result from limma

Gordon K Smyth smyth at wehi.EDU.AU
Thu Aug 14 01:14:38 CEST 2008

OK, I've added sort="none" to the possibilities.

Best wishes

On Wed, 13 Aug 2008, Jenny Drnevich wrote:

> Hi Gordon,
> I guess a sort="none" would be better - I was just thinking about what I have 
> to do, and not what would make the most sense in the function! One advantage 
> of the output from topTable over the fitted model object is that it contains 
> adjusted p-values while the other only contains the raw p-values. I do 
> different manipulations with the topTable results depending on what my 
> clients want, but almost invariably I back calculate to regular fold-changes 
> and remove the t and B columns at the very least. Some want separate "up" and 
> "down" lists, some want me to put "up" and "down" in the output, some want 
> expression levels added, etc.
> Cheers,
> Jenny
> At 06:07 PM 8/12/2008, Gordon K Smyth wrote:
>> Hi Jenny,
>> It would seem a waste to resort toptable by names ... that would 
>> essentially amount to sorting the table, and then unsorting it again. 
>> Something like sort="none" would be better.  Also given that limma handles 
>> data from all sorts of microarray platforms, it always can't be relied on 
>> that the rownames are gene names.
>> My comment about toptable not being the right function, was on the 
>> assumption that anyone creating a toptable of all probes was likely to 
>> write it out to a file.
>> If you find topTable a useful way to get summary statistics for the whole 
>> arrays, that's fine.  What sort fo manipulations do you do with the 
>> toptable in R?  I guess my thought was that most calculations in R would be 
>> done with the fitted model object directly.
>> Best wishes
>> Gordon
>> On Tue, 12 Aug 2008, Jenny Drnevich wrote:
>>> Yeah, now I remember that being in the help page for topTable(). However, 
>>> I'm not sure why it's not the "right" function. Assuming all the arguments 
>>> are equivalent, the values are the same as those output from write.fit(). 
>>> I like topTable() better because it gives you both the raw p-values and 
>>> the adjusted P-values. Maybe it's wrong function because it will give you 
>>> the genes in different orders for each coefficient? I prefer it to 
>>> write.fit so I can work with the values in R without having to read the 
>>> output file back in! However, I do have to re-sort it if I want to use 
>>> with other objects I've created. I've always wanted a resort.by option of 
>>> "gene" that would do my resorting automatically:
>>>> allgenes <- topTable(fit,number=nrow(fit))
>>>> allgenes <- allgenes[order(as.numeric(rownames(allgenes))),]
>>> Any chance of you adding that in the future, Gordon? If not, maybe you can 
>>> expand upon why topTable is not the "right" function.
>>> Thanks!
>>> Jenny
>>> At 02:47 PM 8/12/2008, James W. MacDonald wrote:
>>>> Actually, write.fit() is what you are looking for. From ?topTable:
>>>> Note:
>>>>      This is not the right function to use to create summary statistics
>>>>      for all the probes on an array. Please consider using 'write.fit'
>>>>      or 'write' for this purpose, rather than using 'topTable' with
>>>>      'number=nrow(fit)'.
>>>> ;-P
>>>> Jenny Drnevich wrote:
>>>>> Hi Jixin,
>>>>> You're mixing up the functions topTable() and write.table() and their 
>>>>> arguments. Try this:
>>>>>  > allgenes <- topTable(fit, number= nrow(fit), adjust="BH")
>>>>>  > write.table( allgenes, file= "la.txt")
>>>>> HTH,
>>>>> Jenny
>>>> Jenny Drnevich, Ph.D.
>>>> Functional Genomics Bioinformatics Specialist
>>>> W.M. Keck Center for Comparative and Functional Genomics
>>>> Roy J. Carver Biotechnology Center
>>>> University of Illinois, Urbana-Champaign
>>>> 330 ERML
>>>> 1201 W. Gregory Dr.
>>>> Urbana, IL 61801
>>>> USA
>>>> ph: 217-244-7355
>>>> fax: 217-265-5066
>>>> e-mail: drnevich at illinois.edu 

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