User: Li, Aiguo NIH/NCI

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Posts by Li, Aiguo NIH/NCI

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Comment: C: How to obtain summarized data without normalization
... Thanks, Jim. One more question related to p value I need to generate a fold changes based on only 2 arrays; I like to get a p values associated with fold changes. Which package in R allow me to do this? Thanks, AG On 12/13/10 1:39 PM, "James W. MacDonald" wrote: Hi AG, On 12/10/2010 10:25 ...
written 8.9 years ago by Li, Aiguo NIH/NCI110
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How to obtain summarized data without normalization
... Hi all, I want to get a probeset level data set without mas5 normalization and used the following script. Could someone tell me this is right or not? affydata <- ReadAffy() ExprNonorm<-mas5(affydata,normalize=F) Does these script do the background correction? Or only summarize the probeset ...
normalization written 8.9 years ago by Li, Aiguo NIH/NCI110 • updated 8.9 years ago by James W. MacDonald51k
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Does any one know a package that allow command line dChip normalization with a specific median array?
... Dear Henrick, Wish you had a wonderful holiday season and thank for answering my questions. I have two questions to you. 1. Based on my reading to the information about the aroma.affymetrix, it is designed for analyzing SNP array data. Do you think it will be ok for my case since I need to norm ...
snp normalization written 10.9 years ago by Li, Aiguo NIH/NCI110 • updated 10.9 years ago by Henrik Bengtsson2.4k
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Does any one know a package that allow command line dChip normalization with a specific median array?
... Hello all, I need to normalize expression array from command line using a specific array as baseline median array. Does anybody know a package that allows me to do that? I have checked the expresso package and think that it does not allow me to specify a specific array as median array. Thank ...
written 10.9 years ago by Li, Aiguo NIH/NCI110 • updated 10.9 years ago by Henrik Bengtsson2.4k
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A question related to converting p values to -log p
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written 12.1 years ago by Li, Aiguo NIH/NCI110 • updated 12.1 years ago by Morten Mattingsdal190
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How to make a list as below
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written 12.3 years ago by Li, Aiguo NIH/NCI110 • updated 12.3 years ago by Weiwei Shi1.2k
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A questions related to affymetrix chip normalizationfrom multiple platform
... Hi Adai, Thanks for getting back to me. I have about 100 HGU133A and HGUB and another 100 HGU plus2. I am sure that I can normalize each set separately, then union all of them. My concern will be the batch effects within each set. Can I do a secondary normalization using some simple approach try ...
hgu133a hgu133b gcrma written 13.6 years ago by Li, Aiguo NIH/NCI110
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A questions related to affymetrix chip normalization from multiple platform
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written 13.6 years ago by Li, Aiguo NIH/NCI110 • updated 13.6 years ago by Adaikalavan Ramasamy1.8k
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Questions related to processing large dataset in batches
... Hello, everyone. Our project is a beta tester of Affy HGU133 plus 2 chips, which contain 56,000 probes, and the .cel file size in text format is about 32 MB. We currently have more than 100 chips for data process. I tried to read in the .cel files into my machine (1Gb RAM) and it can only read in ...
normalization probe affy process written 15.4 years ago by Li, Aiguo NIH/NCI110
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A question related to handling large data analysis in bioconducto r
... Hi all. My name is AG LEE, a new bioconductor user. Our project is using HG_U133 plus 2 chips which contain approximately 56,000 probes and the .cel file in text format is about 32MB. Currently we have more than 100 chips and number is growing quickly. I tried to get the data into bioconductor us ...
written 15.4 years ago by Li, Aiguo NIH/NCI110 • updated 15.4 years ago by Tae-Hoon Chung180

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