User: yuabrahamliu

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Posts by yuabrahamliu

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Differential methylation probes were much fewer than differential methylation ge
... Thank you for your reply. ...
written 24 days ago by yuabrahamliu0
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Differential methylation probes were much fewer than differential methylation genes
... Hi everyone, I have a question on differential DNA methylation probes and genes. Hope somebody could give some guidacne. I am working on an EPIC DNA methylation dataset with more than 200 samples (half control samples, and half disease samples), with other confounding information included, like va ...
limma methylation written 28 days ago by yuabrahamliu0 • updated 27 days ago by James W. MacDonald52k
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Comment: C: Limma Design Matrix for Paired Samples with Confouding Factors
... I see. Thank you so much Aaron! ...
written 13 months ago by yuabrahamliu0
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Comment: C: Limma Design Matrix for Paired Samples with Confouding Factors
... Hi Aaron,  I noted a strange thing when fit my data, don't know if it has a large influence on my result. The design matrix I used is,  design <- model.matrix(~ Condition + Source + Pair_Name, data = pd) fit1 <- lmFit(Normdata, design) However, after this step, I will always get a message ...
written 13 months ago by yuabrahamliu0
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Comment: C: Limma Design Matrix for Paired Samples with Confouding Factors
... Learned. Thank you so much Aaron! ...
written 13 months ago by yuabrahamliu0
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Comment: C: Limma Design Matrix for Paired Samples with Confouding Factors
... Hi Aaron, Yes, if consider pairing information and other confounding factors, the effect of Condition should be very limited on regulating gene expression, so I wanted to show the contribution of each factors to the variance using ANOVA,  fit <- aov(logExp ~ Condition + Source + Days + Pair_Na ...
written 13 months ago by yuabrahamliu0
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Comment: C: Limma Design Matrix for Paired Samples with Confouding Factors
... I see. Really learned something. Thank you so much Aaron! ...
written 13 months ago by yuabrahamliu0
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Comment: C: Limma Design Matrix for Paired Samples with Confouding Factors
... Hi Aaron,  Thank you for your help again, but I met a problem when using the method on my data, which is about the pairing information. As shown before, my data are like this, Sample_Name Condition Pair_Name Sample1 Treated 1 Sample2 Control 1 ...
written 13 months ago by yuabrahamliu0
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Comment: C: Limma Design Matrix for Paired Samples with Confouding Factors
... Very helpful. Thank you Aaron! ...
written 13 months ago by yuabrahamliu0
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Limma Design Matrix for Paired Samples with Confouding Factors
... Hi all, I have a data set with both paired samples and confounding factors. I want to use limma to find the differential expressed genes, but I don't know how can I design the design matrix. Could anyone give some suggestions? The data looks like this,  Sample_Name Condition Pair_Na ...
limma design matrix paired samples confounding factors written 13 months ago by yuabrahamliu0 • updated 13 months ago by Aaron Lun25k

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