User: Hua Weng

gravatar for Hua Weng
Hua Weng60
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60
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New User
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Last seen:
14 years, 8 months ago
Joined:
16 years ago
Email:
h****@bmb-fs1.biochem.okstate.edu

Posts by Hua Weng

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Re: Limma: M value in toptable
... Dear Dr. Smyth and Bioconductor members: I have a question about M Values in toptable in LIMMA package. I know the M in toptable is not a simple average from all the replicates, it is a coefficient value from lmFit. I have three biological replicate array and within each array I have six technica ...
written 14.7 years ago by Hua Weng60
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Replicates within array
... Dear Gordon: Thank you very much for your reply. I think we are going to use moderated t-statistic as you suggested. And we are using external controls and spike to do the normalization. I still wondering whether I could use all the replicates on one slide. 6 of them are regular spacing and spacin ...
microarray normalization bayesian written 15.3 years ago by Hua Weng60
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Bayesian method in limma
... Dear Gordon: I tried to use ebayes() method to pick differential expressed genes for our two color cDNA microarray data analysis. Our expreiment is designed to anaylysis the influense of one chemical on cotton genes. It is a Single-Sample Expreiment and two RNA sources are comapred deirectly on 3 b ...
microarray written 15.3 years ago by Hua Weng60 • updated 15.3 years ago by Gordon Smyth39k
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Re: Evaluate correlation beween biological replicates
... Dear All: I am trying to evaluate the correlation between biological replicates. Can I use cor() function in R to calculate correlation of M value after normalization? Is this method appropriate for evaluation? cor(maM(user.norm), use=\"complete\") Thanks in advance Hua [[alternative HTML ...
written 15.7 years ago by Hua Weng60
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Re: read.GenePix() function
... Hi, Jean and everybody: In read.GenePix() function, is there any way I can specify Background Standard Deviation for Cy5 and Cy3( such as B647 SD and B546 SD) in GPR files? user.raw <- read.GenePix(fnames=NULL, path=".", name.Gf="F546 Median", name.Gb="B546 Median", name.Rf="F647 Median", name. ...
written 16.0 years ago by Hua Weng60 • updated 16.0 years ago by Jean Yee Hwa Yang920
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Re: limma package
... Hi, all: I'm trying to read in intensity data in limma package. But I get the following error: > files <- dir(pattern="*\\.gpr") > RG <- read.maimages(files, source="genepix") Error in read.maimages(files, source = "genepix") : Cannot find column heading in image output file I ...
limma written 16.1 years ago by Hua Weng60 • updated 16.1 years ago by Gordon Smyth39k

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