[BioC] "AveExp" column has dissappeared from limma topTable
Mikhail, Amy
a.mikhail at abdn.ac.uk
Mon Apr 2 15:23:45 CEST 2007
Hi Marcus,
"Mosquito" is a subset of my original exprSet (with some probesets taken
out). So it is just a matrix and now that I look, there is no "Amean"
element in my fit object. I didn't know that Amean would not be
derrived for matrices, thanks for pointing that out.
Many thanks,
Amy
-----Original Message-----
From: Marcus Davy [mailto:mdavy at hortresearch.co.nz]
Sent: Monday, April 02, 2007 12:42 AM
To: Mikhail, Amy; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] "AveExp" column has dissappeared from limma topTable
Have a look in your 'fit' object and the lmFit code for clues as to what
is going wrong. When you create a fit object from lmFit, a list element
called 'Amean' may not have been created. This is what is picked up by
topTable.
You didn't mention the structure of the argument object 'Mosquito' in
your lmFit call. Since you have an Affymetrix experiment, is it
"PLMset", "exprSet" "ExpressionSet" or a matrix (unless you used the
convert package to make an MAList)?
If 'Mosquito' is a matrix then a list element for Amean is not created
in your 'fit' object and hence not displayed in topTable
>x <- matrix(1:20, nc=4) #Any old numbers for illustration design <-
>rep(1,4) lmFit(x, design=rep(1,4))$Amean # Amean not created
NULL
> topTable(eBayes(lmFit(x, design)))
logFC t P.Value adj.P.Val B
5 12.5 3.220503 0.001279659 0.006398294 -2.286030
4 11.5 2.962863 0.003047925 0.007619813 -2.696287
3 10.5 2.705222 0.006825866 0.011376444 -3.072355
2 9.5 2.447582 0.014381831 0.017977289 -3.414236
1 8.5 2.189942 0.028528445 0.028528445 -3.721928
Whereas an MAList (or "PLMset", "exprSet" "ExpressionSet") should give
you the AveExpr column. Note: The Amean calculation is not adjusted for
weights, whereas your coefficients are.
>MA <- new("MAList")
>MA$M <- x
>MA$A <- x
>lmFit(MA, design)$Amean # Amean created
[1] 8.5 9.5 10.5 11.5 12.5
> topTable(eBayes(lmFit(MA, design)))
logFC AveExpr t P.Value adj.P.Val B
5 12.5 12.5 3.220503 0.001279659 0.006398294 -2.286030
4 11.5 11.5 2.962863 0.003047925 0.007619813 -2.696287
3 10.5 10.5 2.705222 0.006825866 0.011376444 -3.072355
2 9.5 9.5 2.447582 0.014381831 0.017977289 -3.414236
1 8.5 8.5 2.189942 0.028528445 0.028528445 -3.721928
Hope that helps.
Marcus
On 31/3/07 9:57 AM, "Mikhail, Amy" <a.mikhail at abdn.ac.uk> wrote:
> Dear Bioconductors,
>
> I have a problem with the "AveExp" column in topTable. Usually it
> appears in my toptable output, but during a limma session recently I
> created one toptable (which did have the "AveExp" column in it) and
> then another toptable (which was a subset). In the second topTable,
> the AveExp column was missing. I have tried reloading R, and
> reinstalling limma but the column seems now to be permanently missing
> from my topTables.
>
> There was no error message or warning, so I really don't know what
> I've done ;-(. Sample code is below:
>
>> targets <- readTargets("BaseAgeAffyTargets.txt")
>> targets
> Name FileName Target
> 1 R2s2 AM_041006_R2S2v1_Plasmodium_Anopheles.CEL Adults age 15 days
> 2 R2s6 AM_041006_R2S2_Plasmodium_Anopheles.CEL Adults age 43 days
> 3 R3s2 AM_041006_R3S2_Plasmodium_Anopheles.CEL Adults age 15 days
> 4 R3s6 AM_041006_R3S6_Plasmodium_Anopheles.CEL Adults age 43 days
> 5 R4s2 AM_041006_BAR4Sii_Plasmodium_Anopheles.CEL Adults age 15 days
> 6 R4s6 AM_041006_R4S6_Plasmodium_Anopheles.CEL Adults age 43 days
>>
>> design <- cbind(M15d=c(1,0,1,0,1,0),M43d=c(0,1,0,1,0,1))
>> fit <- lmFit(Mosquito, design)
>> cont.matrix <- makeContrasts(M15dvsM43d=M43d-M15d, levels=design)
>> fit2 <- contrasts.fit(fit, cont.matrix)
>> fit2 <- eBayes(fit2)
>> Lowvar.toptable <- topTable(fit2[ Lowvar.genes, ], number=100,
> adjust="BH")
>
>> Lowvar.toptable[1:8,]
> ID logFC t
> P.Value adj.P.Val B
> 8 Ag.2L.2099.0_CDS_at 0.0525816225 0.613337707
> 0.5608673 0.9967802 -5.844476
> 57 Ag.UNKN.1771.0_CDS_at 0.0514293902 0.602622882
> 0.5675464 0.9967802 -5.851185
> 46 Ag.3R.2483.0_CDS_at 0.0460176987 0.540864707
> 0.6069533 0.9967802 -5.887786
> 24 Ag.2R.3361.0_CDS_at -0.0461903587 -0.540335772
> 0.6072973 0.9967802 -5.888084
> 60 Ag.UNKN.363.0_CDS_at -0.0394899270 -0.464386924 0.6577950
> 0.9967802 -5.928101
> 64 Ag.X.217.0_CDS_a_at -0.0393985675 -0.455020526
> 0.6641680 0.9967802 -5.932647
> 58 Ag.UNKN.1863.0_CDS_at 0.0359376810 0.415978011
> 0.6910563 0.9967802 -5.950663
> 30 Ag.3L.1321.0_CDS_at -0.0334439607 -0.387588909
> 0.7109213 0.9967802 -5.962804
>
> I also note that "A" is also missing from my fit object;
>
>> fit2$Amean
> NULL
>
> I would be most grateful for any suggestions as to what could be
> happening here....
> I realise that I am using R2.4.0 with a more recent version of limma,
> but this has not caused me any problems up until now.
>
> Looking forward to any suggestions,
> Best wishes,
> Amy
>
>
>> sessionInfo()
> R version 2.4.0 (2006-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] "splines" "tools" "methods" "stats" "graphics"
> "grDevices" "utils" "datasets" "base"
>
> other attached packages:
> mixtools mvtnorm agahomology affyPLM gcrma
matchprobes
> affydata annaffy KEGG GO genefilter
> "0.1.0" "0.7-5" "1.14.2" "1.10.0" "2.6.0"
"1.6.0"
> "1.10.0" "1.6.1" "1.14.0" "1.14.0" "1.12.0"
> survival limma geneplotter annotate affy
affyio
> Biobase
> "2.30" "2.9.8" "1.12.0" "1.12.1" "1.12.2"
"1.2.0"
> "1.12.2"
>
> **********************************************************************
> **
> *********************************************************
>
> Amy Mikhail
> Research student
> University of Aberdeen
> Zoology Building
> Tillydrone Avenue
> Aberdeen
> AB24 2TZ
> Scotland
> Email: a.mikhail at abdn.ac.uk
> Phone: 00-44-1224-273256 (office)
>
>
>
>
> [[alternative HTML version deleted]]
>
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