User: Sunny Srivastava

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Posts by Sunny Srivastava

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Comment: C: LIMMA with beta distributed data
... Hi Steve: I think LIMMA does the right thing by not having any link/family because it is meant *only* for log normal intensities. Using it for anything else is not correct. However, as you say you have a lot of 0s -- I would ignore them because you are trying to extract information where it is not ...
written 7.7 years ago by Sunny Srivastava340
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Answer: A: LIMMA with beta distributed data
... Hi Steve: I am sure Prof. Smyth and others will have better insights but here is my $0.02. I would transform the data using the logit transform, that is, x_ij goes to log (x_ij / ( 1 - x_ij) ) ## with boundary value correction when x_ij = 0 or 1 And then use LIMMA. This makes sure that the dat ...
written 7.7 years ago by Sunny Srivastava340
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Calculating average expression value in limma topTable output
... Hello Michael, I am sure more experienced members will have better answers, but here is my $0.02. Your doubt is similar to the doubt I had before. So, hopefully I can answer your question. You are right about the relation between AveExpr and Amean. However, AveExpr is not same as value of the fi ...
probe written 8.0 years ago by Sunny Srivastava340
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Answer: A: Regression using LIMMA
... Hello Somnath: Can you please post some example of the data and the code? It will make help to make your description clearer. If I understand correctly, you are assuming the replicates to be identical; so if rep_1 receives dose_1 and rep_2 receives dose_2, there is no replicate effect for your resp ...
written 8.1 years ago by Sunny Srivastava340
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Answer: A: limma installation trouble
... Hello Anna, I copy pasted the exact commands and installed limma on my ubuntu box. Can you please post the output for sessionInfo() Thanks, S. sessionInfo() -- Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US ...
written 8.1 years ago by Sunny Srivastava340
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Answer: A: limma report logFC confidence interval?
... Hello Thomas, I am sure senior members of the list will have more to say, here is my $0.02. logFC is the coefficient of the treatment in your model. Assuming that you have a model with only one treatment log Int_g = b0 + b1 * trt b1 = logFC The CI of logFC can be found in the same manner as you ...
written 8.1 years ago by Sunny Srivastava340
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limma makeContrasts
... Hello List, I am just forwarding Lorenzo's response to the list as he forgot to copy the list. May be, this is of use in the future. I think, your design is a unbalanced randomized incomplete block design, so it doesn't matter if you have one treatment or multiple for a single block. Also, the dupl ...
go regression limma written 8.2 years ago by Sunny Srivastava340
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Answer: A: limma makeContrasts
... Hello Lorenzo, I am not sure if I understand your question correctly, but here is my $0.02. If you want to account for effect of mother, it would be better include it in your regression model as a factor, but I guess your aim is to detect the difference between DR and NODR (right?). If I understand ...
written 8.2 years ago by Sunny Srivastava340
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Answer: A: Question: How does limma derives its logFC value in two colored arrays?
... Dear Dr. Smyth, Thank you very much for the answer. That clarifies a lot of things! I have one last question to make sure I understood you correctly - in the case of two colored arrays, even if we are regressing the M values on the treatment (sample annotation), we will call the coefficients as lo ...
written 8.2 years ago by Sunny Srivastava340
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Answer: A: applying p.adjust() in limma
... Hello Wei, If I understand your question correctly, most probably tp$adj.P.Val is the adjusted p value for the moderated F statistic (would be different from the moderated t if the number of treatments is more than 2) When you calculate the p-value separately for the three comparisons and use p.ad ...
written 8.2 years ago by Sunny Srivastava340

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Popular Question 7.7 years ago, created a question with more than 1,000 views. For Calculating average expression value in limma topTable output

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