User: Yong Li

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Yong Li50
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Posts by Yong Li

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Model problem using ballgown
... Hello, I am having problems to analyzing an RNA-seq dataset using Ballgown. The RNA are from 3 patients and 3 gender and age matched controls. For each individual there are 3 technical replicates, except for one patient with 6 technical replicates. So there are 21 samples in total. I have processed ...
ballgown linear models written 20 months ago by Yong Li50
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GO enrichment analysis for rice genes
... Dear list members, from an RNA-seq experiment in rice I got a list of differentially expressed genes. I wanted to do a GO enrichment analysis of these genes. The gene IDs are like the following: LOC_Os09g02000.1 LOC_Os07g06834.1 LOC_Os05g36210.1 LOC_Os01g37000.1 ... However it looks like I cannot ...
go written 5.5 years ago by Yong Li50
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arrayQualityMetrics for Agilent one color data
... Dear list members, I have an expression array dataset done with Agilent one color array, and I wanted to do QC using arrayQualityMetrics. I read in the raw Agilent data using limma and background correct and normalization was done according to limma User's guide. This works fine and I got an EList ...
normalization limma arrayqualitymetrics written 6.0 years ago by Yong Li50 • updated 6.0 years ago by James W. MacDonald52k
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Answer: A: Is it recommended to remove control probes for Agilent type data
... Dear Ketaki, it is not good to remove the controls probes before normalization. In normalization step all the data points on the array should be considered. Removing control probes and possible other filtering should be done after normalization, before finding differentially expressed genes. Best ...
written 7.4 years ago by Yong Li50

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