User: Jeremiah H. Savage

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Posts by Jeremiah H. Savage

<prev • 11 results • page 1 of 2 • next >
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Exon ST expression data from GEO
... Hi, I'm wondering what is the best way to get expression data from a GEO entry with the Affymetrix Exon ST platform? For example, I've tried > gse9342 <- getGEO("GSE9342") > head(exprs(gsedat9342[[1]])) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 ^^^ no values are given. I've also t ...
written 7.4 years ago by Jeremiah H. Savage110
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Comment: C: string to function argument
... That does work. Thanks. I also was pointed to a way to do the function call using a string to represent the entire argument: gplaccess <- "gpldata$GPL97" Table(eval(parse(text=gplaccess))) Jeremiah On Wed, Jun 30, 2010 at 3:36 AM, Sean Davis wrote: > You can also do gpldata[["GPL96"]].? I ...
written 7.4 years ago by Jeremiah H. Savage110
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Comment: C: string to function argument
... Hi Sean, I just saw your message after sending the last one a minute ago. My question was that I wanted to use a character object 'gplaccess' that contained the string "gpldata$GPL96" I wanted to use this string to access a data.frame in a GEOData object, but the Table() function expects a GEODat ...
written 7.4 years ago by Jeremiah H. Savage110
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Answer: A: string to function argument
... I just found out that I can access the gpldata list object through [[1]] instead of $GPL96, so the problem is solved. On Tue, Jun 29, 2010 at 4:44 PM, Jeremiah H. Savage wrote: > Hello, > > I would like to get the Table information out of multiple GPLList objects. > > How can I use ...
written 7.4 years ago by Jeremiah H. Savage110
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Answer: A: string to function argument
... One minor correction to the question: gplaccess <- paste("gpldata",gplname,sep="$") Thanks, Jeremiah On Tue, Jun 29, 2010 at 4:44 PM, Jeremiah H. Savage wrote: > Hello, > > I would like to get the Table information out of multiple GPLList objects. > > How can I use a string/cha ...
written 7.4 years ago by Jeremiah H. Savage110
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string to function argument
... Hello, I would like to get the Table information out of multiple GPLList objects. How can I use a string/char variable as a function argument? In this case the function is GEOquery::Table() geodata <- parseGEO("GSExxxx.soft") gpldata <- GPLList(geodata)[1] gplname <- names(gpldata) # e ...
written 7.4 years ago by Jeremiah H. Savage110 • updated 7.4 years ago by Sean Davis21k
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Answer: A: subset GEO data by platform
... I've worked around this problem by doing the following: gplnames <- names(GPLList(geodata)) numgpl <- length(gplnames) gsmdata <- GSMList(geodata) j <- 1 while(j <= numgpl) { accumgsm <- list() for(i in gsmdata) { if( ...
written 7.4 years ago by Jeremiah H. Savage110
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Answer: A: dynamic library() calls
... Never mind, I found the fix: library(gpllibrary,character.only=TRUE) On Mon, Jun 28, 2010 at 4:18 PM, Jeremiah H. Savage < jeremiahsavage@gmail.com> wrote: > I am attempting to use GEOmetadb to select which Affymetrix db to load, but > I get errors from the library() call. > > A ...
written 7.4 years ago by Jeremiah H. Savage110
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dynamic library() calls
... I am attempting to use GEOmetadb to select which Affymetrix db to load, but I get errors from the library() call. Any ideas on what to fix to get this to work? Thank, Jeremiah loadlib <- function() { library(GEOmetadb) if (file.exists("GEOmetadb.sqlite")) { con <- dbConnect ...
geometadb written 7.4 years ago by Jeremiah H. Savage110
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subset GEO data by platform
... I'm working with some data sets which have several platforms, but would like to just work with data from one platform at a time. The code below does NOT work, but it is where I'm at. Can somebody give me a hint on how to modify the lapply() to do what i would like? Thanks, Jeremiah ------------- ...
written 7.4 years ago by Jeremiah H. Savage110 • updated 7.4 years ago by Sean Davis21k

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