User: Timothy Wu

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Timothy Wu120
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Posts by Timothy Wu

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limma report logFC confidence interval?
... On Fri, Oct 29, 2010 at 12:14 PM, Sunny Srivastava wrote: > Hello Thomas, > I am sure senior members of the list will have more to say, here is my > $0.02. > > logFC is the coefficient of the treatment in your model. Assuming that you > have a model with only one treatment > &g ...
regression written 9.0 years ago by Timothy Wu120
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limma report logFC confidence interval?
... HI, Is there a way to report the CI of logFC from topTable in limma? I googled around and it doesn't seem easy to find. I was expecting the option to be in topTable(). Thanks, Timothy [[alternative HTML version deleted]] ...
written 9.1 years ago by Timothy Wu120 • updated 9.1 years ago by Gordon Smyth39k
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Comment: C: Getting annotation into eset
... On Thu, Oct 28, 2010 at 6:34 PM, Sean Davis wrote: > > > On Thu, Oct 28, 2010 at 5:44 AM, Timothy Wu <2huggie@gmail.com> wrote: > >> Hi, >> >> I noticed that when I obtain eset from GEO matrix file via GEOquery, the >> result obtained from limma analysis i ...
written 9.1 years ago by Timothy Wu120
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Getting annotation into eset
... Hi, I noticed that when I obtain eset from GEO matrix file via GEOquery, the result obtained from limma analysis includes the annotation information. However, eset obtained from CEL files via ReadAffy() and GCRMA threestep() do not include those annotations. How do I infuse the annotations into ese ...
limma geoquery written 9.1 years ago by Timothy Wu120 • updated 9.1 years ago by Sean Davis21k
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GEOquery getGEO "error in scan"
... Hi, I'm using getGEO to obtain the serie GSE18154 and I encounter the following error: > gse18154 <- getGEO("GSE18154") Found 1 file(s) GSE18154_series_matrix.txt.gz trying URL ' ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE18154/GSE18154_ser ies_matrix.txt.gz ' ftp data connection ma ...
written 9.6 years ago by Timothy Wu120 • updated 9.6 years ago by Sean Davis21k
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GEOquery, GSE, and MAList
... Hi, Is it possible to convert GSE obtained using getGEO() into an MAList? I tried > gse = getGEO("GSE17308") > ma = GDS2MA(gse) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Meta", for signature "list" GSE is not the same as GDS, so it's no ...
convert written 9.6 years ago by Timothy Wu120 • updated 9.6 years ago by James F. Reid610
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Comment: C: limma topTable columns and new interface?
... Hi Sean, Thanks for the quick reply. On Thu, Apr 15, 2010 at 5:30 PM, Sean Davis 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 & ...
written 9.7 years ago by Timothy Wu120
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limma topTable columns and new interface?
... 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 i ...
affy limma written 9.7 years ago by Timothy Wu120 • updated 9.7 years ago by Sean Davis21k
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Limma design matrix contrast
... Hi, I'm sorry if this this question is probably basic and statistically related. I am analyzing 24 affy slides taken from GEO, 12 slides for each of the two conditions. According to the limma vignetetts chapter 8.5, I can have kinds of two design matrix. What are the differences? So I can either ...
affy limma written 9.7 years ago by Timothy Wu120
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Comment: C: Imitating Affy's own steps
... On Mon, Apr 5, 2010 at 10:24 PM, James W. MacDonald wrote: > Hi Timothy, > > AFAIK, you have two choices. Using the affy package, you can use mas5() and > mas5calls(). You can also use justMAS() from the simpleaffy package. > > I don't believe either one will give you exactly the ...
written 9.7 years ago by Timothy Wu120

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Popular Question 9.0 years ago, created a question with more than 1,000 views. For Getting annotation into eset

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