User: Zhijin Wu

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Zhijin Wu410
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Posts by Zhijin Wu

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Comment: C: GCRMA error
... Do you see "rnu34probe" when you do search() If yes, what do you get if you do P <-get("rnu34probe") On Tue, 10 May 2005, Puhong Gao wrote: > Hi, Zhijin and Jim, > > Thank you both for your quick input. > > Indeed, R automatically initiated the installation of "rnu34cdf" and & ...
written 14.5 years ago by Zhijin Wu410
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Answer: A: GCRMA error
... Please check the probepackage name and cdfpackage name for your chip type first. The ones provided on bioconductor usually have names like "CHIPcdf" and "CHIPprobe" where CHIP is the chip type such as "hgu133a". If your probe package is created with a name following different convention, gcrma may n ...
written 14.5 years ago by Zhijin Wu410
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Answer: A: bg.correct.gcrma?
... Maybe I can include that as an option in the next release. Currently you can modify the gcrma function, at the last line, instead of return(rma(object,background=FALSE,verbose=verbose)) change it to return(object) Then you will get the object before probe level data are normalized and conve ...
written 14.5 years ago by Zhijin Wu410
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Comment: C: Binary CDF file
... where do you get your probe package? try for example, probepkgname="hgu95aprobe" ###change this to your probe package name seq1=get(probepkgname) prlen=nchar(seq1$seq) range(prlen) you should get [1] 25 25 since affy probes are all 25-bases long. The error message you get seems to suggest that you ...
written 14.6 years ago by Zhijin Wu410
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Comment: C: Tiling array application
... Hi, Shinhan, I am afraid I do not have a number to give you. Background will be over estimated when you pass PM intensity and PM affinity instead of MM, as you would expect. When you assume that majority of the PMs mainly contain NSB, hopefully the functional relationship between log(PM-o)~affinity ...
written 14.6 years ago by Zhijin Wu410
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Comment: C: Tiling array application
... To estimate non-specific binding, some negative control probes are desired. However, arrays do not have to have the MM probes as in Affymetrix GeneChip design (one for each PM probe) as negative control probes. They simply should be probes that do not match any specific target in your sample. The ...
written 14.6 years ago by Zhijin Wu410
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Answer: A: gcrma problem
... Since you have a special chip, will you check what "xy2i" function you get with tmp <- get("xy2i", paste("package:", cdfpackagename, sep = "")) Do you have NAs in pmIndex or subIndex? You are right that the line tmp.exprs[pmIndex[subIndex]] = apm is to assign the value from apm to tmp.ex ...
written 14.6 years ago by Zhijin Wu410
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Answer: A: gcrma problem
... You can see the content of function compute.affinities by >compute.affinities #let cdfname be your chip type and cdfname=cdfName(Scoe.m600.exp) verbose=TRUE ## then you can run the content of the function and see where the error happens On Mon, 28 Mar 2005, Wenqiong Chen wrote: > Hi, list: & ...
written 14.6 years ago by Zhijin Wu410
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Answer: A: gcrma() and get() -- oops, 2nd try [sorry for 1st bogus send]
... IT's probably not the problem of "get". Have you installed your probepackage? Where did you install it in? R will try to look online for the packge only when it thinks it's not yet installed. This can happen when 1. it is indeed not installed or 2. it is installed in a directory that R hasn't been t ...
written 14.6 years ago by Zhijin Wu410
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Answer: A: gcrma and custom CDF files : how to make them work together?
... 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 of the function "makeProbePackage". Here's the link http://biocond ...
written 14.6 years ago by Zhijin Wu410

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