User: dorothyc

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dorothyc130
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Posts by dorothyc

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Comment: C: Normalization of expression values
... Thanks so much, Steve! It works now. Dorothy On 2010-07-28, at 9:44 AM, Steve Lianoglou wrote: > By the way .. > > On Tue, Jul 27, 2010 at 7:19 PM, dorothyc wrote: > >> I came across normalize.quantiles {affy} but got the following errors: >> ------ >>> library( ...
written 7.3 years ago by dorothyc130
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Normalization of expression values
... Hi, I'm trying to normalize a table of probe level intensities (pls. see attachment). Would you recommend a method, which would take only a matrix but not an AffyBatch or object and do quantile normalization, in R/Bioconductor packages. I came across normalize.quantiles {affy} but got the followi ...
normalization probe written 7.3 years ago by dorothyc130 • updated 7.3 years ago by Steve Lianoglou12k
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Comment: C: Installing affy package
... Hi Seth and Keith, It works now. Thanks very much for your help. Regards, Dorothy On Nov 24, 2009, at 8:59 PM, Seth Falcon wrote: > On 11/24/09 5:20 PM, Keith Satterley wrote: >> Hi Dorothy, >> >> I'm not sure about the smootScatter error. Sometimes these sort of >> t ...
written 8.0 years ago by dorothyc130
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Installing affy package
... Hi, I've been experiencing problems installing the affy package (please see output below). I've installed the latest versions of Biobase and affyio already. Thanks very much!! Regards, Dorothy ############# ~/% R CMD INSTALL affy_1.24.2.tar.gz * Installing to library '/home/dorothyc/R/x86_64-un ...
biobase affy written 8.0 years ago by dorothyc130 • updated 8.0 years ago by Keith Satterley450
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Bar plots with stacked columns marked with askterisks
... Hi, I'm trying to plot bar graphs with stacked columns marked with askterisks for certain columns, which follow certain criteria. I've gotten the stacked bar plots with Data set A (please refer to code below and plot attached). However, I haven't figured how to put asterisks on columns based on s ...
written 8.3 years ago by dorothyc130 • updated 8.3 years ago by Fraser Sim270
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Mfuzz plot -pdf
... Hi, I'm trying to make pdf for mfuzzPlot (please see script below), but I keep getting an error saying the file is not recognizable or corrupted (please see attachment). The mfuzzPlot can be displayed in R but not written as a PDF?! ---------------------- mfuzzPlot <- mfuzz.plot(eset.s, cl = c ...
mfuzz written 8.6 years ago by dorothyc130 • updated 8.6 years ago by James W. MacDonald45k
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Mfuzz package
... Hi, I'm trying out the Mfuzz package for soft clustering. I've encountered an error (please see below). I'd be really grateful if you could shed some light. > filename <- my_table > my.data <- read.table(filename, sep="\t") > set <-new("ExpressionSet", exprs = as.matrix(my.d ...
clustering mfuzz written 8.6 years ago by dorothyc130 • updated 8.6 years ago by James W. MacDonald45k
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Annotation for Mouse 430 2.0 and Human Genome U133 Plus 2.0 Arrays
... Hi, I'd like to know if there are any changes in the annotation information for the mouse430a vs mouse430a.db packages for the Mouse 430 2.0 array and that for hgu133plus2 vs hgu133plus2.db packages for the Human Genome U133 Plus 2.0 array. Thanks, Dorothy ...
hgu133plus2 written 8.8 years ago by dorothyc130 • updated 8.8 years ago by Marc Carlson7.2k
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simpleaffy with hgu133plus2
... Hi, I'm trying to do simpleaffy pairwise comparison on hgu133plus2 data. However, I'm running into problems with results.summary() (please see below). It didn't recognize hgu133plus2 because the package now is called hgu133plus2.db. But when I assigned "hgu133plus2.db" to "arrayid", I got another ...
hgu133plus2 simpleaffy written 8.9 years ago by dorothyc130
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Answer: A: Prokaryotic_Rhodobacter capsulatus GEP
... Hi Jim, Thanks very much for your advice. It works now. Regards, Dorothy On Dec 1, 2008, at 5:41 AM, James W. MacDonald wrote: > Looking at the output that the OP has provided implies to me that > she used the makecdfenv package to create a cdf package, but > installed it incorrectly. ...
written 9.0 years ago by dorothyc130

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