User: Moshe Olshansky

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Posts by Moshe Olshansky

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Answer: A: lumi - construct a design matrix
... Hi Paolo, Your command: colnames(design) <- c('CME','ES','CMA','CMN') is wrong (i.e. this is not what model.matrix produces). Do the two previous commands, i.e. sampleType <- c('CME','ES','CMA','CMN','CME','ES','CMA','CMN','CME','ES','CMA','CMN' ) design <- model.matrix(~ factor(sample ...
written 7.1 years ago by Moshe Olshansky250
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Comment: C: design matrix Limma design for paired t-test
... Hi Ingrid, If I understand correctly, you would like to find genes which are differentially expressed (DE) between Treatment and Control at 4 hours and compare them with those which are DE at 18 hours. One way to do it is to split your data into two separate sets ( 4 hours and 18 hours) and find DE ...
written 7.2 years ago by Moshe Olshansky250
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Comment: C: design matrix Limma design for paired t-test
... Hi Ingrid, With your design your "base" level is patient 4, Control, 4 hours (let's call it B). The mean for, say, patient 6, Treatment, 18 hours is: B + Donor6 + TreatT + Time18 where Donor6 is the difference between Donor4 and Donor6 (same for any treatment and time), TreatT is the difference bet ...
written 7.2 years ago by Moshe Olshansky250
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Comment: C: necessity of moderated t statistic and false discoveries for small predefined ge
... Hi Rich, You have already got the answer from Kasper. This is exactly what I am suggesting. The idea is that after log transformation the variances of the genes follow some distribution. So the more genes you are using the better you can estimate that distribution. This is just a model, nobody is c ...
written 7.3 years ago by Moshe Olshansky250
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Comment: C: necessity of moderated t statistic and false discoveries for small predefined ge
... Hi Rich, I think that Gordon Smyth (the author of limma) has explained at this list what moderated t-statistic is. The brief explanation is that when there are few samples the estimate of the variance which is used in a standard t-test is quite noisy and because one must account for this noise the ...
written 7.3 years ago by Moshe Olshansky250
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Answer: A: necessity of moderated t statistic and false discoveries for small predefined ge
... Hi Rich, Whether to use the moderated t-statistic or not does not depend on whether you are interested in the 10 particular genes or in all differentially expressed ones. This will affect your multiple testing adjustment. The simplest way for you to proceed is to use limma as usual, get the topTabl ...
written 7.3 years ago by Moshe Olshansky250
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Answer: A: Random Forest Code
... Here is the link to the original Fortran 77 code: http://www.stat.berkeley.edu/~breiman/RandomForests/cc_examples/prog.f See also http://www.stat.berkeley.edu/~breiman/RandomForests/ The R package should probably contain the wrapper code (but ask the package creator). Best regards, Moshe. > D ...
written 7.3 years ago by Moshe Olshansky250
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Comment: C: [Limma] lmFit handle missing value in phenotype
... You are right. My mistake. Sorry... > Hi, Moshe, > > I still did not get it. How to use your method? > > lmFit<-(x,design) which x allow missing values, but design didn't. > > usually, I want to adjust batch effects, I will include it in design > matrix, i.e. > ...
written 7.4 years ago by Moshe Olshansky250
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Answer: A: plausibility of cyclic loess normalization on multiple experiment
... You can definitely use cyclic loess normalization for one channel arrays unless your experiments are very different, in which case any normalization can be problematic. Moshe. > Dear all, > > Is it plausible to do cyclic loess normalization on single channel > arrays coming from differ ...
written 7.4 years ago by Moshe Olshansky250
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Answer: A: [Limma] lmFit handle missing value in phenotype
... Why do you want to include weight in the design matrix? It may be more reasonable to include weight in the linear model, i.e. expression ~ condition + weight and then your design matrix will have two columns (if there are two conditions): the first column will contain 0's and 1's depending on the co ...
written 7.4 years ago by Moshe Olshansky250

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