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@abdn.ac.uk
Phone: 00-44-1224-273256 (office)

 


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