[BioC] How to save result from limma
J.delasHeras at ed.ac.uk
J.delasHeras at ed.ac.uk
Wed Aug 13 13:37:19 CEST 2008
Indeed, I prefer to use the output of topTable too, I select what I
want from it, and create my results files from it.
I'm not sure it's a question of "right" or "wrong", but more of a
preference...
Jose
Quoting Cei Abreu-Goodger <cei at sanger.ac.uk>:
> In many cases, I tend to prefer the topTable output if only for the
> reason that the "ID" column comes first (I know, a very poor reason).
> Is there any strong reason why we should never use topTable for full
> output? I thought that, at least for single contrasts, the information
> is the same than what can be obtained by write.fit. Also, having a
> data.frame object helps manipulation prior to saving as a file.
>
> Cei
>
> 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………………….…………. 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 18 592
>>>> 1 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
>>> 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
>>
>
>
> --
> Cei Abreu-Goodger, PhD
>
> Wellcome Trust Sanger Institute
> Computational and Functional Genomics
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, CB10 1SA, UK
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
> _______________________________________________
> 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
--
Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
More information about the Bioconductor
mailing list