[BioC] "AveExp" column has dissappeared from limma topTable
Marcus Davy
mdavy at hortresearch.co.nz
Mon Apr 2 01:42:15 CEST 2007
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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