User: Chuming Chen

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Chuming Chen140
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Posts by Chuming Chen

<prev • 13 results • page 1 of 2 • next >
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access Limma objects
... Hi All, Is there a way to get the normalized log mean intensity values from the limma analysis, and then to rank order these values from 1 to 100? Thanks, Chuming ...
limma written 6.1 years ago by Chuming Chen140 • updated 6.1 years ago by James W. MacDonald47k
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Comment: C: DEXSeq error
... Dear Wolfgang, I have downloaded DEXSeq 1.3.9 and tested using my data. Everything is fine now. Thanks for this nice tools and quick fix. Chuming On Jul 12, 2012, at 7:57 AM, Wolfgang Huber wrote: > Dear Chuming > > Thank you for your message. The current version of DEXSeq is 1.3.9: &g ...
written 6.1 years ago by Chuming Chen140
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Comment: C: DEXSeq error
... Hi Alejandro, Thanks a lot for your quick reply! Please see my answers to your questions below. On Jul 6, 2012, at 12:33 PM, Alejandro Reyes wrote: > Dear Chuming Chen, > > Thanks for the report, it was not so clear to me in which part of your code the error message comes out, but I thin ...
written 6.1 years ago by Chuming Chen140
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DEXSeq error
... Hi All, I am trying to use DEXSeq to find out differential exon usage and encounter the following error. I have included the session info and my R script. Could you please help me finding out what could be the problem? Estimating Cox-Reid exon dispersion estimates using 30 cores. (Progress repor ...
dexseq written 6.1 years ago by Chuming Chen140 • updated 6.1 years ago by Alejandro Reyes1.6k
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cytoband.Rdata for chicken genome
... Dear All, I am running CGHweb locally to analysis NimbleGen Whole genome CGH design for chicken (galGal3). My code stopped with the error message "Invalid genome type", it turns out that cytoband.RData in the CGHweb package does not include cytoband data for chicken genome. Where can I find cytob ...
written 8.5 years ago by Chuming Chen140
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Comment: C: Agilent G4112A Arrays
... Prashantha and everybody comments on my question: Thank you very much! Chuming Prashantha Hebbar wrote: > Hi Chuming, > > I have over looked your previous mail. It seems, there is nothing > wrong. So, better to follow Wolfgang and Naomi suggestions. > > Regards, > Prashantha ...
written 8.6 years ago by Chuming Chen140
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Comment: C: Agilent G4112A Arrays
... Prashantha and all, Here is the sessional information regarding my analysis of this data set. Can you point out what I might do wrong? Thanks, Chuming > library(limma) > > targets <- readTargets("Targets.txt") > targets SlideNumber Name FileName ...
written 8.6 years ago by Chuming Chen140
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Comment: C: Agilent G4112A Arrays
... Hi Francois: The experiment was done five years old. I am just trying to do some analysis. This experiment was performed on human colonic crypts. They were microdissected into two parts - the top 9/10 and the bottom 1/10. Thus in my target file, T or B stands for top or bottom and the number afte ...
written 8.6 years ago by Chuming Chen140
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Comment: C: Agilent G4112A Arrays
... Hi Prashantha, Thank you for your suggestion. My target file is as below. Although I couldn't fit a linear model, I still wonder whether I can do some statistic on M (log ratio) values and use the p-value to get the differentially expressed genes. SlideNumber FileName Cy3 Cy5 1 B1vsT1. ...
written 8.6 years ago by Chuming Chen140
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Agilent G4112A Arrays
... Dear All, I am trying to find out the differentially expressed genes from some Agilent Human Whole Genome (G4112A) Arrays data. I have tried LIMMA package, but LIMMA gave the error message "no residual degrees of freedom in linear model fits" and stopped. My guess is that my data has no replicates ...
limma written 8.6 years ago by Chuming Chen140 • updated 8.6 years ago by Prashantha Hebbar260

Latest awards to Chuming Chen

Popular Question 6.1 years ago, created a question with more than 1,000 views. For Agilent 2-color Microarray data analysis tutorial

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