limma topTable columns and new interface?
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Timothy Wu ▴ 120
@timothy-wu-3964
Last seen 10.3 years ago
Hi, In Limma I run topTable for Affy chips. After write.table(), there are 8 columns of data, but only 7 headers (and they are misplaced to the left by 1 position). The last column "B" is log odd, correct? What is the data in the first column? Also, the topTable help says "toptable is an earlier interface and is retained only for backward compatibility." So is it deprecated? What is the new interface? Timothy [[alternative HTML version deleted]]
affy limma affy limma • 1.3k views
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@sean-davis-490
Last seen 4 months ago
United States
On Thu, Apr 15, 2010 at 5:17 AM, Timothy Wu <2huggie at gmail.com> wrote: > Hi, Hi, Timothy. > In Limma I run topTable for Affy chips. After write.table(), there are 8 > columns of data, but only 7 headers (and they are misplaced to the left by 1 > position). The last column "B" is log odd, correct? What is the data in the > first column? These are the row names in the first column. See the help for write.table(). > Also, the topTable help says "toptable is an earlier interface and is > retained only for backward compatibility." So is it deprecated? What is the > new interface? toptable and topTable() are two different functions. I believe the latter version is preferred over the former. Hope that helps. Sean
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Hi Sean, Thanks for the quick reply. On Thu, Apr 15, 2010 at 5:30 PM, Sean Davis <seandavi@gmail.com> wrote: > On Thu, Apr 15, 2010 at 5:17 AM, Timothy Wu <2huggie@gmail.com> wrote: > > Hi, > > Hi, Timothy. > > > In Limma I run topTable for Affy chips. After write.table(), there are 8 > > columns of data, but only 7 headers (and they are misplaced to the left > by 1 > > position). The last column "B" is log odd, correct? What is the data in > the > > first column? > > These are the row names in the first column. See the help for > write.table(). > > topTable(fit2, adjust.method="BH", number=10) ID logFC AveExpr t P.Value adj.P.Val B 12861 203413_at -4.863939 9.063835 -17.02642 5.096458e-16 2.786489e-11 25.33969 16463 207016_s_at -8.002118 7.819954 -15.55356 4.768779e-15 1.303665e-10 23.44225 10459 201010_s_at -4.086280 10.489258 -14.17960 4.503602e-14 8.207815e-10 21.48528 34429 225171_at -3.855857 10.257294 -13.88007 7.514060e-14 1.027078e-09 21.03252 15016 205568_at -4.293815 7.765863 -12.14548 1.733606e-12 1.648261e-08 18.20875 14531 205083_at -4.907075 7.403553 -12.12315 1.808792e-12 1.648261e-08 18.17003 51083 241833_at -6.651936 5.153752 -11.57349 5.234556e-12 4.088562e-08 17.19685 32874 223597_at -7.323707 8.198642 -11.33152 8.448496e-12 5.774019e-08 16.75594 14094 204646_at -3.634998 9.030261 -11.03786 1.524340e-11 9.260368e-08 16.21036 11291 201842_s_at -4.967125 9.415506 -10.94798 1.829875e-11 1.000484e-07 16.04104 This is after topTable and before write.table(), I don't know what the first column means. I checked the Limma vignette, it doesn't seem to say. The topTable() help says there are, geneList, logFC, avgExpr, t, F (omitted unless more than one coef is specified), P.Value, adj.P.Value, and B. I don't see the column label for the first column. > > > Also, the topTable help says "toptable is an earlier interface and is > > retained only for backward compatibility." So is it deprecated? What is > the > > new interface? > > toptable and topTable() are two different functions. I believe the > latter version is preferred over the former. > > Oh! I see. :) Timothy [[alternative HTML version deleted]]
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---------- Forwarded message ---------- From: Timothy Wu <2huggie@gmail.com> Date: Thu, Apr 15, 2010 at 5:45 AM Subject: Re: [BioC] limma topTable columns and new interface? To: Sean Davis <seandavi@gmail.com> Cc: bioconductor@stat.math.ethz.ch Hi Sean, Thanks for the quick reply. On Thu, Apr 15, 2010 at 5:30 PM, Sean Davis <seandavi@gmail.com> wrote: > > On Thu, Apr 15, 2010 at 5:17 AM, Timothy Wu <2huggie@gmail.com> wrote: > > Hi, > > Hi, Timothy. > > > In Limma I run topTable for Affy chips. After write.table(), there are 8 > > columns of data, but only 7 headers (and they are misplaced to the left by 1 > > position). The last column "B" is log odd, correct? What is the data in the > > first column? > > These are the row names in the first column. See the help for write.table(). > topTable(fit2, adjust.method="BH", number=10) > ID logFC AveExpr t P.Value > adj.P.Val B > 12861 203413_at -4.863939 9.063835 -17.02642 5.096458e-16 2.786489e-11 > 25.33969 > 16463 207016_s_at -8.002118 7.819954 -15.55356 4.768779e-15 1.303665e-10 > 23.44225 > 10459 201010_s_at -4.086280 10.489258 -14.17960 4.503602e-14 8.207815e-10 > 21.48528 > 34429 225171_at -3.855857 10.257294 -13.88007 7.514060e-14 1.027078e-09 > 21.03252 > 15016 205568_at -4.293815 7.765863 -12.14548 1.733606e-12 1.648261e-08 > 18.20875 > 14531 205083_at -4.907075 7.403553 -12.12315 1.808792e-12 1.648261e-08 > 18.17003 > 51083 241833_at -6.651936 5.153752 -11.57349 5.234556e-12 4.088562e-08 > 17.19685 > 32874 223597_at -7.323707 8.198642 -11.33152 8.448496e-12 5.774019e-08 > 16.75594 > 14094 204646_at -3.634998 9.030261 -11.03786 1.524340e-11 9.260368e-08 > 16.21036 > 11291 201842_s_at -4.967125 9.415506 -10.94798 1.829875e-11 1.000484e-07 > 16.04104 > > This is after topTable and before write.table(), I don't know what the > first column means. I checked the Limma vignette, it doesn't seem to say. > The topTable() help says there are, geneList, logFC, avgExpr, t, F (omitted > unless more than one coef is specified), P.Value, adj.P.Value, and B. I > don't see the column label for the first column. > The first "column" is not a column. It contain row names. They are not part of the data but are only labels for the rows. Sean > > > Also, the topTable help says "toptable is an earlier interface and is > > retained only for backward compatibility." So is it deprecated? What is the > > new interface? > > toptable and topTable() are two different functions. I believe the > latter version is preferred over the former. > Oh! I see. :) Timothy [[alternative HTML version deleted]]
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> This is after topTable and before write.table(), I don't know what the first > column means. I checked the Limma vignette, it doesn't seem to say. The > topTable() help says there are, geneList, logFC, avgExpr, t, F (omitted > unless more than one coef is specified), P.Value, adj.P.Value, and B. I > don't see the column label for the first column. These are the row names of the matrix. You can suppress this by using write.table( ..., row.names=FALSE ). Then you will have exactly the same number of columns and column names. See help( "write.table" ). j. -- -------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web : www.mpiib-berlin.mpg.de Tel : +49-30-28460514
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