User: Lizhe Xu

gravatar for Lizhe Xu
Lizhe Xu210
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210
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Last seen:
14 years, 2 months ago
Joined:
15 years, 8 months ago
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l**@chnola-research.org

Posts by Lizhe Xu

<prev • 21 results • page 1 of 3 • next >
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Need help to creat AffyBatch object
... We come out with new idea of normalization and tested on Affy U95 serial dilution data set. As a result of the normalization, we got a matrix: row as probe (PM intensity) (the probe of the same probe set are adjacent and if there are more than 16 probe sets, we only keep the first 16); column as dif ...
normalization probe affy written 14.2 years ago by Lizhe Xu210 • updated 14.2 years ago by Kasper Daniel Hansen6.4k
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BioC 1.4 MAS implementation
... Please help me with the MAS method. I got more than half of the probe sets with value as NA (16645 for U133A) after using the following command: > set<-expresso(data, normalize.method="constant", bgcorrect.method="mas", pmcorrect.method="subtractmm",summary.method="mas") background correction ...
probe written 15.1 years ago by Lizhe Xu210 • updated 15.1 years ago by James W. MacDonald51k
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Expresso command error
... I thought that the following command in previous version of BioC was working, but with new version I got an error. So I must be wrong, what should the correct command be? Thanks. > set<-expresso(data, normalize.method="invariantset", bg.correct.method="mas", pmcorrect.method="pmonly",summary. ...
written 15.1 years ago by Lizhe Xu210 • updated 15.1 years ago by Wolfgang Huber13k
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Error message in RMA
... I got the following error when using RMA command: > data<-ReadAffy() > data AffyBatch object size of arrays=712x712 features (23767 kb) cdf=HG-U133B (22645 affyids) number of samples=6 number of genes=22645 annotation=hgu133b Warning message: package hgu133bcdf was built under R version 2. ...
cdf written 15.1 years ago by Lizhe Xu210
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Bionconductor1.4 vs R1.9 and R2.0
... Hi, I want to install bioconductor on my new computer but cannot find the R 1.9. The link in Bioconductor installation page is down and the web page of R provides only R 2.0. I wonder if Bioconductor 1.4 works under R 2.0. If not, please help me find a place to download the R 1.9 for window. Thanks ...
written 15.1 years ago by Lizhe Xu210 • updated 15.1 years ago by Vincent J. Carey, Jr.6.3k
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dChip
... Thanks, I did not notice that difference, but how was bioconductor bgcorrect=MAS method implemented, 10 by 10 or 4 by 4? I did both MAS with Affy software and MAS in bioconductor on the same data set and got quite different results. I wonder if the difference comes from the background correction. L ...
affy written 15.1 years ago by Lizhe Xu210
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dChip
... Hi, The Li and Wong method uses the .cel file generated by MAS. What I believed the bg.correct=MAS in order to exactly mimic it. I don't know why to use bg.correct=FALSE in your analysis. Thanks. L. Ann, A more exact way to mimic the Li and Wong method with the command expresso is: expresso(affy ...
written 15.1 years ago by Lizhe Xu210 • updated 15.1 years ago by Ben Bolstad1.1k
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MAS vs gcrma, rma and Li-Wong method in Affy package for TC study
... I have recently started to use bioconduct to analyze a time course study with U133A and B, which has 7 time points including time zero (T0). Each time point has three replicates and every one is compared to T0. With R 1.8.1 and affy package 1.3.28, I tested gcrma, rma, Li-Wong algorithm (PM only, s ...
normalization clustering affy gcrma genespring written 15.7 years ago by Lizhe Xu210
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mas5calls Problem
... I really don't know if there is a problem or not for the background correction. I don't have anything to compare with it, at least there is no error displayed on the screen. For the flag, since I have a filter results on flag from Affy DMT, I compared it with the output of the Affy package and found ...
microarray affy written 15.7 years ago by Lizhe Xu210
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Problem with mas5calls, bugs?
... After using the rma, I used mas5calls to read the flag call from Affy U133A .txt file. But I was surprised to find that the mas5calls got quite different results compared to the original .txt file (798 inconsistance for 22283 probe sets for a group of 6 arrays, when comparing with the DMT). Is it so ...
probe written 15.7 years ago by Lizhe Xu210

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