[BioC] Extracting expressions after a multtest procedure (part2)
J. Miguel Marin
jmmarin at est-econ.uc3m.es
Wed Mar 19 18:52:59 CET 2008
Hello,
I think this is a valuable information.
Best
----- Mensaje reenviado de jmmarin at est-econ.uc3m.es -----
Fecha: Mon, 17 Mar 2008 23:59:59 +0100
De: "J. Miguel Marin" <jmmarin at est-econ.uc3m.es>
Responder-A: "J. Miguel Marin" <jmmarin at est-econ.uc3m.es>
Asunto: Re: [BioC] Extracting expressions after a multtest procedure (part2)
Para: Martin Morgan <mtmorgan at fhcrc.org>
Hello Martin,
you are absolutely right.
In fact, I need to identify just the correct genes because I am
searching for significant differences in expressions in order to
calculate distances among the same genes in "BCR/ABL" group and in
"NEG" group.
Thank you very much again for your help.
Best.
> JUAN MIGUEL MARIN DIAZARAQUE wrote:
>> Helo Martin,
>>
>> In fact when I wrote
>>
>>> idx1 = res$index[res$adjp[,"BH"]<0.05,]
>> Error in res$index[res$adjp[, "BH"] < 0.05, ] : incorrect number of
>> dimensions
>
> I guess that should have been idx1=res$index[ res$adjp[,"BH"]<0.05] ]
>
> I know that Sean's suggestion works, in the sense that you get an
> answer. I was not quite sure that it was the right answer -- res$adjp
> is ordered from highest significance to lowest significance. When you
>
> idx2 = res$adjp[,"BH"]<0.05
>
> you get a logical vector (TRUE and FALSE values), probably all the
> first ones are TRUE and all the later ones FALSE (because adjp was
> ordered that way).
>
> > head(idx2, n=110)
> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> [25] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> [37] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> [49] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> [61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> [73] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> [85] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> [97] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
> [109] FALSE FALSE
>
> Now when you subset exprs(esetSub)[idx2,], you select all the rows of
> exprs(esetSub) for which the corresponding entry in idx2 is 'TRUE'.
> But since the order of genes in res$adjp is different from the order
> of genes in exprs(esetSub), you won't get the right genes.
>
> Martin
>
>> Anyway, thank you very much for your help.
>>
>> Cheers
>>
>>> Off list, because I am not sure, but from the docs I think there
>>> might be a couple of redirections
>>>
>>> idx1 = res$index[res$adjp[,"BH"]<0.05,]
>>>
>>> to get to resT[idx,], and maybe a second (or using the rownames) to
>>> get back to the ExpressionSet.
>>>
>>> If you figure it out, Juan, and if there is a correction, it would
>>> be good to post to the list again.
>>>
>>> Martin
>>>
>>> Sean Davis wrote:
>>>> On Sun, Mar 16, 2008 at 11:56 AM, JUAN MIGUEL MARIN DIAZARAQUE
>>>> <jmmarin at est-econ.uc3m.es> wrote:
>>>>> Hello,
>>>>>
>>>>> In previous message I wonder how to extract just the expressions of 102
>>>>> genes under two conditions after a multtest procedure.
>>>>>
>>>>> At last, I wrote this unelegant code that seems to work:
>>>>>
>>>>> quedan <- resT[res$adjp[,"BH"]<0.05,]
>>>>> busco <- dimnames(quedan)[[1]]
>>>>>
>>>>> cosa <- NULL
>>>>> for (i in 1:length(dimnames(exprs(esetSub))[[1]]))
>>>>> for (j in 1:length(busco))
>>>>> if (dimnames(exprs(esetSub[i,]))[[1]] == busco[j]) {
>>>>> cosa <- rbind(cosa, as.data.frame(exprs(esetSub))[i,]) }
>>>>> end
>>>>> end
>>>>
>>>> Generally, you can subset ExpressionSets just like you do data frames;
>>>> rows are genes or probes and columns are samples. If esetSub is what
>>>> you used for your multtest procedure, you should be able to do:
>>>>
>>>> exprs(esetSub)[res$adjp[,'BH']<0.05,]
>>>>
>>>> In general, for loops are quite useful in R, but for things like
>>>> subsetting or vectorized operations, it is better to look for other
>>>> alternatives as they are likely to be faster.
>>>>
>>>> Sean
>>>>
>>>> _______________________________________________
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>>>
>>>
>>
>>
>>
>>
>> jm~
>>
>> _______________________________
>>
>> Juan Miguel Marin
>>
>> http://www.est.uc3m.es/jmmarin
>>
>> Dep. of Statistics
>> University Carlos III of Madrid
>> Spain (E.U.)
>> _______________________________
>>
>>
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>
jm~
_______________________________
J. Miguel Marin
http://www.est.uc3m.es/jmmarin
Dep. of Statistics
University Carlos III of Madrid
Spain (E.U.)
_______________________________
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