[BioC] How to save result from limma

[Jenny Drnevich]

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 
>_______________________________________________ 
>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