User: Sunny Srivastava
Sunny Srivastava • 340
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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 8.0 years ago by
Sunny Srivastava • 340
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... 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 8.0 years ago by
Sunny Srivastava • 340
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... 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 ...
written 8.3 years ago by
Sunny Srivastava • 340
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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 8.4 years ago by
Sunny Srivastava • 340
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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 8.4 years ago by
Sunny Srivastava • 340
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... 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 8.4 years ago by
Sunny Srivastava • 340
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... 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 ...
written 8.5 years ago by
Sunny Srivastava • 340
0
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1
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Answer:
A: limma makeContrasts
... Hello Lorenzo,
I am not sure if I understand your question correctly, but here is my
$0.02.
If you want to account for effect of mother, it would be better
include it
in your regression model as a factor, but I guess your aim is to
detect the
difference between DR and NODR (right?). If I understand ...
written 8.5 years ago by
Sunny Srivastava • 340
0
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1
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... Dear Dr. Smyth,
Thank you very much for the answer.
That clarifies a lot of things!
I have one last question to make sure I understood you correctly - in
the
case of two colored arrays, even if we are regressing the M values on
the
treatment (sample annotation), we will call the coefficients as lo ...
written 8.5 years ago by
Sunny Srivastava • 340
0
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Answer:
A: applying p.adjust() in limma
... Hello Wei,
If I understand your question correctly, most probably
tp$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 8.5 years ago by
Sunny Srivastava • 340
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For Calculating average expression value in limma topTable output
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