User: yuabrahamliu

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Posts by yuabrahamliu

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Comment: C: Limma Design Matrix for Paired Samples with Confouding Factors
... I see. Thank you so much Aaron! ...
written 5 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 5 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 6 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 6 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 6 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 6 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 6 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 6 months ago by yuabrahamliu0 • updated 6 months ago by Aaron Lun23k
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Job: Bioinformatic Postdoc Position at University of Michigan
... Description Dr. Lana Garmire's translational bioinformatics group in the Department of Computational Medicine and Bioinformatics at University of Michigan has multiple postdoc positions for highly competent and motivated researchers immediately. Current projects include (1) Single-cell genomics and ...
job postdoc bioinformatic written 6 months ago by yuabrahamliu0
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Comment: C: How can I define which samples are controls and which samples are cases in ChAMP
... I see. Thank you Yuan! ...
written 6 months ago by yuabrahamliu0

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