[BioC] How to save result from limma

Tue Aug 12 22:16:14 CEST 2008

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
>>At 01:58 PM 8/12/2008, Wang, Jixin wrote:
>>>Dear all, I am using limma to analyze my 
>>>microarray data. I have a simple question to 
>>>ask. I want to save the summary table of ALL 
>>>genes into local drive. I had tried to use 
>>>write, write.table or save command but I 
>>>always got error message. 
>>>write.table(topTable, "la.txt") Error in 
>>>as.data.frame.default(x[[i]], optional = TRUE) :
>>>Cannot coerce class "function" into a 
>>>data.frame 
>>>write.table(fit,number=100,adjust="BH",file="la.txt") 
>>>Error in write.table(fit, number = 100, adjust = "BH", file = "la.txt") :
>>>unused argument(s) (number = 100, adjust = 
>>>"BH") When I use write.table (fit, 
>>>file="la.txt"), I got something like this: 
>>>"coefficients" "stdev.unscaled" "sigma" 
>>>"df.residual" "genes.Block" "genes.Row" 
>>>"genes.Column" "genes.ID" "genes.Name" "Amean" 
>>>"s2.post" "t" "p.value" "lods" "F" "F.p.value" 
>>>"1" 0.191491534183039 0.5 0.58043881130755 3 1 
>>>1 1 5103 NA 6.32074826791933 0.303968848417341 
>>>0.694648392759644 0.509374409393106 
>>>-4.86326047572600 0.482536389563556 
>>>0.509374409393106 "2" -0.293787384283484 0.5 
>>>1.20366297838960 3 1 1 2 5124 NA 
>>>8.24502874291735 0.774060196679415 
>>>-0.667845140479293 0.525351390376272 
>>>-4.87400797979679 0.446017131661806 
>>>0.525351390376272 "3" -0.513890138933438 0.5 
>>>0.298947585330255 3 1 1 3 5145 NA 
>>>6.24632903576038 0.199313133368442 
>>>-2.30214313044810 0.0543270719852833 
>>>-3.89174526089124 5.29986299306939 
>>>0.0543270719852833 "4" -0.192900665446982 0.5 
>>>0.202699077289498 3 1 1 4 5166 NA 
>>>5.4719589146908 0.178899971606802 
>>>-0.912133876540687 0.391633127283331 
>>>-4.76408991981505 0.831988208733142 
>>>0.391633127283331 "5" -0.519787414790754 0.5 
>>>0.971899999883875 3 1 1 5 5187 NA 
>>>4.79242047112468 0.560886278852435 
>>>-1.38809230856769 0.207129224092528 
>>>-4.49088947369315 1.92680025710479 
>>>0.207129224092528

.â€¦â€¦â€¦â€¦. What I 
>>>want is same as below (contain logFC, P Value and adj.P.Val) of ALL genes,
>>>options(digits=3) 
>>>topTable(fit,number=100,adjust="BH")     Block 
>>>Row Column    ID Name logFC 
>>>AveExpr     t  P.Value adj.P.Val     B 
>>>20830    46   2     18  5921   NA  3.22    8.42 15.76 8.78e-07
>>>0.0195 -1.78 5073     11  21     13 
>>>15499   NA  3.09   11.56 12.58 
>>>4.15e-06    0.0460 -1.86 6457     14  21     11  9451   NA  2.93
>>>10.48 10.88 1.11e-05    0.0617 -1.93 4193     10   2     13  9974
>>>NA  2.69   10.25 10.87 1.11e-05    0.0617 -1.93 292       1  14
>>>6  5195   NA  2.22    9.67 10.35 1.55e-05    0.0689 -1.95 12237    27
>>>11      5 13493   NA  3.80    8.45  9.17 
>>>3.46e-05    0.1145 -2.03 
>>>15180    33  18     22  1831   NA  4.62    9.16 9.11 3.61e-05
>>>0.1145 -2.03 

 ¦â€¦â€¦â€¦ Many thanks, 
>>>Jixin 
>>>_______________________________________________ 
>>>  Bioconductor mailing list 
>>>Bioconductor at stat.math.ethz.ch 
>>>https://stat.ethz.ch/mailman/listinfo/bioconductor 
>>>Search the archives: 
>>>http://news.gmane.org/gmane.science.biology.informatics.conductor
>>_______________________________________________
>>Bioconductor mailing list
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>
>--
>James W. MacDonald, M.S.
>Biostatistician
>Hildebrandt Lab
>8220D MSRB III
>1150 W. Medical Center Drive
>Ann Arbor MI 48109-0646
>734-936-8662

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 