User: payam_delfani1980

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Posts by payam_delfani1980

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Comment: C: Creating a correct limma model with respect to contrast matrix and design matrix
... Dear Aaron, I compared the approach you suggested here to that of the makeAllContrasts from EMA package, and can say that both method generate same outputs. However, the advantage of makeAllContrasts is that it creates the contrasts while keeping the original name of annotations. ...
written 15 months ago by payam_delfani19800
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Creating a correct limma model with respect to contrast matrix and design matrix
... I am trying fit a linear model with limma, where I do adjust for a batch variable. Then I want o calculate statistics for all pair-wise comparisons. Here, I'm wondering whether the way I create the model and its contrast-fits make sense and looks correct. Could anyone consider the example below and ...
limma limma design matrix limma contrast matrix written 15 months ago by payam_delfani19800 • updated 15 months ago by Aaron Lun25k
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Comment: C: Is there an equivalent function for write.fit() that produces values/output in R
... I also wanted to report that I found that write.fit() generates, among other outputs, a variable named "Coef" which is actually the Fold Change (FC). I also suggest to revise the name of variable to avoid any miss-interpretation of that variable.  ...
written 15 months ago by payam_delfani19800
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Comment: C: Is there an equivalent function for write.fit() that produces values/output in R
... Thank you for your quick reply, Sir! I've tested the two functions that you outlined above. Unfortunately, show() and as.data.frame() do not fully produce the same output as write.fit () does. The output differs because write.fit() can further process the testResults when the user provides argument ...
written 15 months ago by payam_delfani19800
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Is there an equivalent function for write.fit() that produces values/output in R console?
... write.fit() in limma is an excellent function that writes a MArrayLM Object to a File. Using this function, no value is produced in R console but a file is written to the current working directory. I'm wondering if there is an equivalent function for write.fit() that produces values/output in the sa ...
limma write.fit written 15 months ago by payam_delfani19800 • updated 15 months ago by Gordon Smyth39k
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Computing se.exprs in R for an Expressionset?
... Hi How to compute se.exprs (standard errors for the expression estimates) in R for an Expressionset? ...
microarray expressionset se.exprs written 15 months ago by payam_delfani19800

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