User: BioLite

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BioLite20
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Posts by BioLite

<prev • 30 results • page 3 of 3 • next >
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Comment: C: Why my limma DEG result in top Table all without significant meaning,showing log
... Dear Gordon, Actually, I worked with limma at first. However, I couldn't understand the probe filter part in the user guide. Following your tips, I will analysis with limma again. Thanks! ...
written 17 months ago by BioLite20
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Comment: C: Why my limma DEG result in top Table all without significant meaning,showing log
... Yes, thanks for your sweet tip, I will notice my code layout next time. ...
written 17 months ago by BioLite20
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Comment: C: Why my limma DEG result in top Table all without significant meaning,showing log
... Yes, Fabio. Q1, 27 PD, and 26 control samples; Q2, my analysis data from this published article,https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002794. The bad samples have been removed by the authors, I get the cleaned data from ArrayExpress,https://www.ebi.ac.uk/arrayexpre ...
written 17 months ago by BioLite20
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Comment: C: Why my limma DEG result in top Table all without significant meaning,showing log
... Kevin, thank you very much! Devon and Fabio both experienced than me, I will learn modestly from them. Thanks again, wish you have a good day! ...
written 17 months ago by BioLite20
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Comment: C: Why my limma DEG result in top Table all without significant meaning,showing log
... Nothing. I just checked my code again, finding some wrongs. So sad, I always make mistakes. Let me correct it and then discuss with you. Devon, thanks for your caring! Have a good day! BTW, my data from this article,https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002794. I ...
written 17 months ago by BioLite20
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Comment: C: Why my limma DEG result in top Table all without significant meaning,showing log
... Here is my complete code, really hope to get some help. rm(list = ls()) setwd("E:/Practice/Aglient/PD") library(Agi4x44PreProcess) library(hgug4112a.db) library(limma) ##loading data targets<-read.targets("targets.txt") raw_data<-read.AgilentFE(targets = t ...
written 17 months ago by BioLite20 • updated 17 months ago by genomax78k
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Comment: C: Why my limma DEG result in top Table all without significant meaning,showing log
... Yes Kevin, thank for your answer. But my key question still alive. Once I set parameter lfc=1.5, summary(dt_result) showing Diff Down 0 NotSig 38822 Up 0 That's because of my topTable results with no changes, with nothing significant expression. I really don't know how ...
written 17 months ago by BioLite20
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Why my limma DEG result in top Table all without significant meaning,showing logFC <1.5 or logFC>-1.5 ?
... Hi, all I'm a newbie, and I'm dealing with Agilent single channel microarray when I filtering DEGs using limma, I find all my results showing logFC>-1.5 or logFC<1.5, without significant expression. I have been searching reason for a long time, but I still don't know what my faults are, I real ...
;logfc limma deg toptable written 17 months ago by BioLite20
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Comment: C: gene filtering for agilent microarray using Limma
... OH! So happy! Kevin answered this question! I am a newbie and have been concerned about Agilent single channel microarray analysis question for a long time. But I still bothered by some questions. All remarks on Biostar show Kevin you are always kindful and helpful, may I borrow some your precious t ...
written 18 months ago by BioLite20 • updated 18 months ago by zx87549.0k
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Comment: A: gene filtering for agilent microarray using Limma
... sad, nothing improvement? ...
written 18 months ago by BioLite20

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