User: Fangxin Hong

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Fangxin Hong810
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Posts by Fangxin Hong

<prev • 81 results • page 1 of 9 • next >
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Answer: A: outlier removal from gene chip
... Dear Weiwei, The definition of outlier is not clear, and no data point should be treated as outlier unless there is reason to believe so. The simple way to detect it is that 1.5IQR criteria, which you can write your own code (one or two lines). Update me if there are any other method to detect outli ...
written 11.2 years ago by Fangxin Hong810
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Answer: A: Linear models with different platforms
... If you are interested in finding DE (differetially expressed ) genes, you can try RankProd, which combines data from different platforms without assuming equal variance. For linear model without assuming equal variance, it sounds to me that you shouldn't use one linear model since you won't gain an ...
written 11.7 years ago by Fangxin Hong810
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Comment: C: Arabidopsis annotation package
... Hi Ting-Yuan, Thank you for your reply. > > The package ath1121501 (version 1.10.0) is built by the public data we > collected on September 29, 2005. Any updated information on the data > website after September 29, 2005 would not be included in the package > ath1121501 (version 1. ...
written 11.7 years ago by Fangxin Hong810
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Arabidopsis annotation package
... Hi there, I met some questions about arabidopsis annotation package(ath1121501, version 1.10), I will be truly grateful if any of you can help me with some questions. (1) I tried to get PUBMED ID for probesets (Affy) that have known function and known pubmed ID from website. However, the "ath112 ...
annotation annotate written 11.7 years ago by Fangxin Hong810 • updated 11.7 years ago by Ting-Yuan Liu FHCRC780
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Comment: C: Analysis for only 2 replicates
... Based on my experience,SAM usually fails with only 2 replicates under each condition. Limma and RankProd both can handle 2 replicates. Fangxin > > > > On 3/8/06 4:07 PM, "Khan, Sohail" wrote: > >> Dear list, >> >> I have 2 -wt and 2-mutant samples done on Affymetr ...
written 11.7 years ago by Fangxin Hong810
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Answer: A: Analysis for only 2 replicates
... try Rankprod which is based on fold change but with much more power. Fangxin > Dear list, > > I have 2 -wt and 2-mutant samples done on Affymetrix chips. > Could you suggest the best way to analyze this experiment? Is averaging > both replicates and picking genes based on fold chang ...
written 11.7 years ago by Fangxin Hong810
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Answer: A: Rank Product
... Hi Nadine, > 1. I tried to calculate the Rank product in Excell (as explain in the > paper > of Rainer Breitling) using a small data set, i didn't get the same > results > as calculating it with R-Programm. > Can somebody help me? The RankProd package under bioconductor is progra ...
written 11.7 years ago by Fangxin Hong810
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ath1121501 package updated?
... Hi list, Does anyone know whether ath1121501 package has been updated to include additional information, such as "ath1121501CHRLENGTHS" ? Without it, geneplotter package is not applicable. I think such informaion is available from TAIR. Thanks! Fangxin -------------------- Fangxin Hong Ph.D. P ...
ath1121501 written 11.8 years ago by Fangxin Hong810 • updated 11.8 years ago by Ting-Yuan Liu FHCRC780
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Comment: C: Biological replication (was RNA degradation problem)
... Thank you all for the useful input and interesting discussion. I agree with Henk, "biologicla replicates" means to include biological variation among individual plants, not the enviromental factors, such as growth chamber and climate. It is known that batch effect and lab effect are profound factor ...
written 11.8 years ago by Fangxin Hong810
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Answer: A: RNA degradation problem
... Hi Matthew, Thank you very much for your help. > It's amazing how many > lab plant biologists see pooled samples from a bulk of plants grown at > the same time as biological replicates when they are clearly not. I would think that all plants under experiment shoudl be grown at the same ti ...
written 11.8 years ago by Fangxin Hong810

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