User: gregory.l.stone

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Posts by gregory.l.stone

<prev • 57 results • page 1 of 6 • next >
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Comment: C: limma: how to use pairing and adjust for covariates
... You're right! I apologize for my carelessness. However, if I am not specifying an intercept, don't I need the pre terms in my design so that I can make a contrast like the following: con <- makeContrasts(sexDiff = "(sexFemale_conditionpost - sexFemale_conditionpre) - (sexMale_conditionpost - sexM ...
written 2.2 years ago by gregory.l.stone10
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Comment: C: limma: how to use pairing and adjust for covariates
... When I block on patient in the design I now find I get the following message when normalizing with voom: > v = voomWithQualityWeights(dge, design, plot=FALSE) Coefficients not estimable: sexMale.conditionpost sexFemale.conditionpost The same message prints repeatedly. I have samples for each co ...
written 2.2 years ago by gregory.l.stone10
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Comment: C: limma: how to use pairing and adjust for covariates
... When I make my contrast matrix (following con <- makeContrasts(sexDiff = "sexFemale_conditionpost - sexMale_conditionpost", levels=design)), I get the following message: Warning message: In makeContrasts(sexDiff = "sexFemale_conditionpost - sexMale_conditionpost",  : Renaming (Intercept) to Inter ...
written 2.2 years ago by gregory.l.stone10
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limma: how to use pairing and adjust for covariates
... I am interested in looking at the differences in the effect of a condition on each sex. The contrast I am interested in is (Female.post - Female.pre) - (Male.post - Male.pre). I am uncertain as to how best incorporate pairing into my study and adjust for covariates. One way I have tried to incorpor ...
limma limma paired analysis limma contrast matrix limma-voom written 2.2 years ago by gregory.l.stone10 • updated 2.2 years ago by Aaron Lun24k
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Comment: C: remove batch effect and adjusted model for 4 covariates in Limma
... Does the presence of an intercept make it so that each patient term is relative to the first patient term? For example, isn't the column "patientB" in the design matrix is actually patientB relative to patientA? If so, does this still accomplish the intended blocking effect?   ...
written 2.2 years ago by gregory.l.stone10
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Comment: C: Multiple testing limma contrasts
... Ok, thank you for the clarification ...
written 2.3 years ago by gregory.l.stone10
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Comment: C: Multiple testing limma contrasts
... I have read that section, but am confused due to the fact that my contrast of interest is a contrast of contrasts. I understand that toptable corrects for the contrast of interest, and using "global" in decideTests would work for me because I am considering multiple contrasts, but there is no parame ...
written 2.3 years ago by gregory.l.stone10
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Comment: C: Multiple testing limma contrasts
... Additionally, when I designate method as "separate" I get no sig genes from decideTests, but when I designate method as "global" I get hundreds. However, when I use toptable to collect the gene names and logFC, I get no sig genes after BH correction. Am I doing something incorrectly? ...
written 2.3 years ago by gregory.l.stone10
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Multiple testing limma contrasts
... I am using limma-voom to determine the change in the change of gene expression between men and women due to a treatment. I have previously received great help on this site, and am confident in my workflow up until choosing a method to do multiple testing correction int he decideTests method. I don't ...
limma multiple testing correction limma voom limma contrast matrix written 2.3 years ago by gregory.l.stone10 • updated 2.3 years ago by James W. MacDonald50k
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Comment: C: limma and edgeR QL strange results
... Yea, that must've been a copy-paste mistake. Thank you so much again for the extensive help and for being so generous with your time.   ...
written 2.3 years ago by gregory.l.stone10

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