[BioC] How to save result from limma

[James W. MacDonald]

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………………….…………. 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 
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> 
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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
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