Question: "AveExp" column has dissappeared from limma topTable
0
gravatar for Marcus Davy
12.6 years ago by
Marcus Davy680
Marcus Davy680 wrote:
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]] > > _______________________________________________ > 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 ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}
ADD COMMENTlink modified 12.6 years ago by Gordon Smyth38k • written 12.6 years ago by Marcus Davy680
Answer: "AveExp" column has dissappeared from limma topTable
0
gravatar for Amy Mikhail
12.6 years ago by
Amy Mikhail460
Amy Mikhail460 wrote:
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@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]] > > _______________________________________________ > 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 ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}
ADD COMMENTlink written 12.6 years ago by Amy Mikhail460
Answer: "AveExp" column has dissappeared from limma topTable
0
gravatar for Gordon Smyth
12.6 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:
Dear Amy, See https://www.stat.math.ethz.ch/pipermail/bioconductor/2007-February/0 16132.html Note that 'Amean' is the older name for 'AveExpr'. Best wishes Gordon > Date: Mon, 2 Apr 2007 14:23:45 +0100 > From: "Mikhail, Amy" <a.mikhail at="" abdn.ac.uk=""> > Subject: Re: [BioC] "AveExp" column has dissappeared from limma > topTable > To: "Marcus Davy" <mdavy at="" hortresearch.co.nz=""> > Cc: bioconductor at stat.math.ethz.ch > > 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) ---------------------------- Dr Gordon K Smyth, Research Fellow, Bioinformatics, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3050, Australia Tel: (03) 9345 2326, Fax (03) 9347 0852, Email: smyth at wehi.edu.au, www: http://www.statsci.org
ADD COMMENTlink written 12.6 years ago by Gordon Smyth38k
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