User: Richard Finney

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Posts by Richard Finney

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hthgu133a + gcrma = pms error
... Using a recent version of R, I get an error running gcrma on hthgu133a (high throughput Affymetrix U133A) chips. The error is Error in pms[, i] <- GSB.adj(Yin = pms[, i], subset = index.affinities, : number of items to replace is not a multiple of replacement length Calls: gcrma -> ...
gcrma written 9.4 years ago by Richard Finney180
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hthgu133adim not found
... When running gcrma on htghu133a chips, I get this error message: Computing affinities.Error in get(x, envir, mode, inherits) : variable "hthgu133adim" was not found Execution halted Anybody got any idea what's wrong? I'm running Linux/R2.5 Gory details here ... uname -a Linux lxxxxxxx.xxx.xxx.gov ...
gcrma written 9.4 years ago by Richard Finney180 • updated 9.4 years ago by James W. MacDonald45k
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Answer: A: Problems with affycomp - quantile.default
... I'm getting a mysterious error message "no slot of name "exprs" for this object of class "AffyBatch"" Anybody got any ideas on what crime I committed? I got the latest greatest Bioconductor stuff yesterday. The gory details ... -bash-3.00$ uname -a Linux xxxxx.yyy.nih.gov 2.6.9-42.0.3.ELsmp #1 S ...
written 10.3 years ago by Richard Finney180
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Comment: C: metadata - annotation package changes
... Previously I have been using R Version 2.0.1 on a Linux box as root and everything worked well. I have installed in my local user director the latest R Version 2.1.1 on a different machine (a Sun box) from the source code and I am not running as root. I can't quite figure out how to make getBioC() ...
written 12.3 years ago by Richard Finney180
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Comment: C: Missing probesets
... note: cutz'n'snips are from previous paye/gentleman emails ... > > be ok but when i read my cel files I realise that > about 20% of my > > probesets are missing. Which expression algorihtm are you using? MAS5 chops off high/low (i.e. two) probes for each probeset; so probesets with ...
written 12.5 years ago by Richard Finney180
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gcrma() and get() -- oops, 2nd try [sorry for 1st bogus send]
... Thanks, Zhijin, I have, through a backdoor, created the probepackage for a custom CDF. I do have a second question: gcrma() uses the get() function/method. Is there a way to force get() to look locally and not in the "repository" out on the internet? I can't quite figure out the invocation of this ...
cdf probe gcrma written 12.7 years ago by Richard Finney180 • updated 12.7 years ago by Zhijin Wu410
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gcrma() and get()
... --- Zhijin Wu wrote: > Hi, > > gcrma uses probe sequence information in estimating > non-specific binding > so you need the probepackge. You can create the > probepackge if it's not > available on bioconductor. The vignette for > 'matchprobes" package has > description o ...
cdf probe gcrma written 12.7 years ago by Richard Finney180
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gcrma and custom CDF files : how to make them work together?
... I am having a little trouble torturing gcrma() into accepting a custom CDF file created locally. (Local in this case is R Ver 2.0.1 on a reasonably recent linux box). I can create and convince R/Bioc to accept a custom CDF file in some cases. It works fine with rma() and mas5() . But ... gcrma us ...
cdf written 12.7 years ago by Richard Finney180 • updated 12.7 years ago by Zhijin Wu410
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Answer: A: Custom CDF Files - howto ?
... Rhonda, I wrote a program that takes an original text CDF file as a template and writes out my revised "units" (Affyspeak for probesets). The revised units are sets of probes that map to a quality filtered set of transcripts: higher quality transcripts, chimerics stripped, latest Genbank records ...
written 12.8 years ago by Richard Finney180
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Comment: C: affy Yeast 2.0 annotation
... I have created a custom CDF file. The purpose is to measure the expression of splice variations. I place the file in the same directory as the CEL files and crank up R and do the usual BIOC incantation. Based on a suggestion offered by the brainiacs at University of Michigan ( http://brainarray. ...
written 12.8 years ago by Richard Finney180

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