User: Puhong Gao

gravatar for Puhong Gao
Puhong Gao140
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14 years, 3 months ago
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16 years, 9 months ago
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p***@hunter.cuny.edu

Posts by Puhong Gao

<prev • 14 results • page 1 of 2 • next >
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Answer: A: GCRMA error
... Hi, Zhijin, I don't see "rnu34probe" and other chip packages (see below) > search() [1] ".GlobalEnv" "package:splines" "package:gcrma" [4] "package:matchprobes" "package:affy" "package:reposTools" [7] "package:Biobase" "package:tools" "package:methods" [10] "pa ...
written 14.3 years ago by Puhong Gao140
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Answer: A: GCRMA error
... Hi, Zhijin and Jim, Thank you both for your quick input. Indeed, R automatically initiated the installation of "rnu34cdf" and "rnu34probe" when I first ran GCRMA. Since I got the posted error, I manually installed rnu34 packages downloaded from Bioconductor site and got the same error when GCRMA ...
written 14.3 years ago by Puhong Gao140
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GCRMA error
... Hi, all, When I ran my old chip data (RN U34 chips) with gcrma, I got the following error. I had no problem with other chip types. Can someone give me some inputs on this? Thank you. > gcrma.ob<-gcrma(ob) Computing affinitiesError in get(x, envir, mode, inherits) : variable "rnu34probe" was ...
gcrma written 14.3 years ago by Puhong Gao140
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Re: MvA plotting error
... Got rid of the error after R was restarted. Puhong ----- Original Message ----- From: Puhong Gao To: bioconductor@stat.math.ethz.ch Sent: Thursday, March 17, 2005 2:27 PM Subject: MvA plotting error Hi, all, The following error message was generated when I used "mva.pairs()" functio ...
written 14.4 years ago by Puhong Gao140
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MvA plotting error
... Hi, all, The following error message was generated when I used "mva.pairs()" function to plot my data. "Error in simpleLoess(y, x, w, span, degree, parametric, drop.square, normalize, : recursive default argument reference" The same message was given when the example in the Help file was ...
written 14.4 years ago by Puhong Gao140
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Help with LPE error message
... Hi, all, When I ran LPE test on my 100 datasets, I got the following error message on two of the 100 tests. Can someone help me out of what the possible cause(s) is? Thank you. "Error in var(M[vect.temp], na.rm = TRUE) : `x' is empty" The analysis failed at the step when "baseOlig.error()" was c ...
lpe written 14.5 years ago by Puhong Gao140 • updated 14.5 years ago by Jain, Nitin70
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Question: Background correction using sequence info!
... Hi, all, I'd like to background correct my data using sequence info and then to explore them with different normalization algorithms, vsn and quantiles, for examples. Has anyone ever tried it this way? Can someone give some suggestions of how to do that? Thank you in advance for your help. I perfo ...
normalization vsn gcrma written 15.5 years ago by Puhong Gao140
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Answer: A: How to modify an Affybatch object?
... Got it! Many thanks to Rafael and Johannes for their help. Best, Puhong ----- Original Message ----- From: "Rafael A. Irizarry" To: "Puhong Gao" Cc: Sent: Monday, March 01, 2004 1:28 PM Subject: Re: [BioC] How to modify an Affybatch object? > you can use the pm method, e.g to put the mean ...
written 15.5 years ago by Puhong Gao140
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How to modify an Affybatch object?
... Hi, all, Is it possible to insert the modified PM values back to the original affybatch and then to normalize it? I'd like to use the averaged intensities of my technical replicates to normalize against other biological replicates. Any comments and/or suggestions will be very appreciated. Thank yo ...
written 15.5 years ago by Puhong Gao140
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Test version of gcrma!
... Hi, Jean, Could you send me a copy of the test version of gcrma too? I am having problems with the released version--memory problem. I have tried unsuccessfully to run gcrma on the data from 60 RG-U34a chips (all versions of R and bioconductor packages); but it was OK for data from 30 chips. Thank ...
gcrma written 15.6 years ago by Puhong Gao140

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