User: KJ Lim

gravatar for KJ Lim
KJ Lim420
Reputation:
420
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Trusted
Location:
Finland
Last seen:
4 years, 6 months ago
Joined:
7 years, 6 months ago
Email:
j*********@gmail.com

Posts by KJ Lim

<prev • 42 results • page 1 of 5 • next >
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Comment: C: edgeR: glmLRT test
... Dear Jim, Good day and thanks for your prompt replied. This brings us to a pedantic discussion of what a p-value means, what a > statistical test is actually testing, etc. This is in general boring for > non statisticians, but is a fairly critical point that people should > understand. &g ...
written 6.6 years ago by KJ Lim420
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Comment: C: edgeR: glmLRT test
... Dear Jim and community, I read the Limma User's Guide and read again the edgeR User's Guide. I believe the section 3.5 "Comparison both Between and Within Subjects" in the edgeR User's Guide is suitable to answer my question: Do phenotypes HS & LS have effect on the area (SW is control)? I c ...
written 6.6 years ago by KJ Lim420
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Comment: C: edgeR: glmLRT test
... Dear Jim, Thanks for your prompt relied and suggestion. I will have a look on the Limma User's Guide. Thank you. Best regards, KJ Lim On 22 March 2013 17:28, James W. MacDonald wrote: > Hi KJ, > > > On 3/22/2013 11:17 AM, KJ Lim wrote: > >> Dear Jim, >> >> Tha ...
written 6.6 years ago by KJ Lim420
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Comment: C: edgeR: glmLRT test
... Dear Jim, Thanks for your replied. I used read.delim to read my data into R session. The target object is: files phenotype area 1 H3TZ.txt HS TZ 2 H3SW.txt HS SW 3 H4TZ.txt HS TZ 4 H4SW.txt HS SW 5 L2TZ.txt LS TZ 6 L2SW.txt ...
written 6.6 years ago by KJ Lim420
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edgeR: glmLRT test
... Dear edgeR community, Good day. I have sets of RNA-Seq data of 2 phenotype (HighS, LowS) plants with area TZ & SW (control). I used exactTest to study which genes that are differential expressed in area TZ compare to SW of each phenotype. I would like to know do the phenotypes have effect on ...
edger written 6.6 years ago by KJ Lim420 • updated 6.6 years ago by James W. MacDonald51k
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Comment: C: edgeR: estimateGLMTrendDisp or estimateGLMCommonDisp
... Dear Prof Gordon, Thanks for your suggestion. Have a nice day. Best regards, KJ Lim On 25 January 2013 03:21, Gordon K Smyth wrote: > Dear KJ Lim, > > It may depend on the specific data, but I think that > > y <- estimateGLMCommonDisp(y,**design) > y <- estimateGLMT ...
written 6.8 years ago by KJ Lim420
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edgeR: estimateGLMTrendDisp or estimateGLMCommonDisp
... Dear edgeR community, Good day. Please forgive me if I ask a stupid question. May I ask, using trended dispersion to estimate genewise (tagwise) dispersion for multi factors experiment design is better than using common dispersion? Thanks for your time and advice. Best regards, KJ Lim ...
edger written 6.8 years ago by KJ Lim420 • updated 6.8 years ago by Gordon Smyth39k
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Answer: A: edgeR version
... Dear Guiling Sun, You should able to see the version of edgeR in the Bioconductor -edgeR web page . Scroll down and have a look on "Details" section. Alternatively, use sessionInfo() to learn version of installed edgeR package after loaded edgeR into R session. Hopefully this help. Best regard ...
written 6.8 years ago by KJ Lim420
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Answer: A: Drastic change in edgeR p-value calculation?
... Dear Lee, Hopefully this archive thread is useful to your case: Differences in results between two different versions of edgeR https://stat.ethz.ch/pipermail/bioconductor/2012-December/049644.html Best regards, KJ Lim On 18 December 2012 20:35, Lionel (Lee) Brooks 3rd < Lionel.Brooks.GR@dart ...
written 6.9 years ago by KJ Lim420
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Comment: C: GO annotation
... Dear Marc, Thanks for your prompt replied. Your information is helpful. You are right about the organism I'm working on. It is not a model species nor human samples, it is a gymnosperm plant species. I will have a look on the ?makeOrgPackageFromNCBI package from the manual, hopefully I have luck ...
written 7.1 years ago by KJ Lim420

Latest awards to KJ Lim

Popular Question 4.5 years ago, created a question with more than 1,000 views. For edgeR: estimateGLMTrendDisp or estimateGLMCommonDisp
Great Question 4.5 years ago, created a question with more than 5,000 views. For edgeR: Value of variation of biological variation (BCV)
Popular Question 4.5 years ago, created a question with more than 1,000 views. For edgeR: topTags
Popular Question 4.5 years ago, created a question with more than 1,000 views. For edgeR : input and design matrix help
Popular Question 4.5 years ago, created a question with more than 1,000 views. For edgeR: Value of variation of biological variation (BCV)
Popular Question 4.5 years ago, created a question with more than 1,000 views. For edgeR: topTags
Popular Question 4.5 years ago, created a question with more than 1,000 views. For edgeR: Value of variation of biological variation (BCV)

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