User: yao chen

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yao chen200
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Posts by yao chen

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[Limma] Can I adjust family relationship in Limma?
... Hi all, I have thousands samples from different families. Now I want to find differential expressed gene using Limma. I have family correlation matrix from kinship, Is there any way I can include these correlation in lmFit? Thanks, Jack [[alternative HTML version deleted]] ...
limma written 5.3 years ago by yao chen200
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Comment: C: Testing for no difference
... I am not an expert of statistic. Why not use ANOVA? Jack 2012/7/23 Wolfgang Huber > > Btw, a less complex way to approach such an analysis is highlighted here: > > http://nsaunders.wordpress.**com/2012/07/23/we-really-dont-** > care-what-statistical-method-**you- used/ > > ...
written 5.3 years ago by yao chen200
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[LIMMA]lmFit with continuous predictor
... Hi all, I am trying to use Limma for multiple regression. The design matrix is like this : EffectA EffectB 1 25 0 35 0 28 1 32 The Effect A is categorical, The Effec ...
regression limma written 5.4 years ago by yao chen200 • updated 5.4 years ago by Belinda Phipson120
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Answer: A: Affy mas5 scaling
... Hi Liat, Personally, I will use RMA instead of MAS5 to normalization affy data. It's quite normal when you use different parameter in normalization, you get different number of genes. But it's not a big problem. I would expect highly overlap of these two sets of genes. Jack 2012/7/12 Liat S &g ...
written 5.4 years ago by yao chen200
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Comment: C: #Identify differentially expressed genes
... Hi Paolo, Did you still use "colnames(design) <- c('A','B','C','D')"? 2012/7/12 Paolo Kunderfranco > Thanks but there is still something that i miss, here is the code that > I used, I set up sampletype, 4 samples, in triplicates, respect to the > position if the dataMatrix with my n ...
written 5.4 years ago by yao chen200
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Answer: A: #Identify differentially expressed genes
... Hi Paolo, You just need to put all 4 groups in the design matrix. It's a clear example in the Limma userguide.: > f <- factor(targets$Target, levels=c("RNA1","RNA2","RNA3")) > design <- model.matrix(~0+f) > colnames(design) <- c("RNA1","RNA2","RNA3") To make all pair-wise compari ...
written 5.4 years ago by yao chen200
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Answer: A: GO enrichment significance
... Hi Mark, One thing you should notice is the hierarchy structure of Gene Ontoloty. You may find two different terms are actually child-parent terms. Therefore it may not be many "different" terms for genes within a cluster. You may use some software to find the specific term accounting for the hier ...
written 5.4 years ago by yao chen200
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Answer: A: help with multiple testing
... Hi Mike, I think another reason is the small sample size and many gene pairs.So randomly significant pairs would be expect which generate high FDR. I don't know if there is a better solution. I would choose top ranking genes with big fold change and small p value. Jack 2012/6/25 efthimiosm & ...
written 5.4 years ago by yao chen200
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Comment: C: [Limma] Calculate the relation between mRNA and miRNA
... Hi Belinda, I know what you mean. But I also want to include the treatment factor. The linear model is mRNA=miRNA+treatment+miRNA*treatment. So I can't use simple correlation. Jack 2012/6/22 Belinda Phipson > Hi Jack > > I think you have misunderstood what lmFit does. lmFit takes t ...
written 5.4 years ago by yao chen200
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[Limma] Calculate the relation between mRNA and miRNA
... Hi all, I have a problem to use lmFit calculated the correlation between mRNA and miRNA, because my miRNA data contained "NA" values. So if I use :lmFit(mRNA,miRNA), I got the message "Error in qr.default(x) : NA/NaN/Inf in foreign function call (arg 1)". The original "lm" function allow to inclu ...
mirna written 5.4 years ago by yao chen200 • updated 5.4 years ago by Belinda Phipson120

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Popular Question 5.3 years ago, created a question with more than 1,000 views. For [LIMMA]lmFit with continuous predictor

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