## User: wewolski

wewolski10
Reputation:
10
Status:
New User
Location:
Zurich
Last seen:
1 month, 1 week ago
Joined:
4 years, 2 months ago
Email:
w*******@gmail.com

#### Posts by wewolski

<prev • 11 results • page 1 of 2 • next >
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... _You need the residual variance (also known as residual standard error or residual mean square) and the residual df._ These - residual standard error, residual df - I do have for each model. Obviously, I than could then run the squeezeVar function as intended. But then how do I update the std:Er ...
written 6 months ago by wewolski10
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... Dear Gordon, The table is not the table of a single model on one subject but, the result of running the same model on several hundred of subjects and then computing the same contrast on all models. I updated my post to clarify this a bit more. Sorry that it wasn't more precise, I updated it accord ...
written 6 months ago by wewolski10
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... Hello, I do have a data frame my_dataframe with parameter estimates (i.e. linear combinations of the model parameters - contrasts). "ID" "Contrast" "Estimate" "Std. Error" "df" "t-value" "lower" "upper" "Pr(>|t|)" 1 "A - B" 3.2 .... ...
written 6 months ago by wewolski10
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... Daer Forum, I want to get an estimate of the pairing variable BioReplicate What I would do when using linear model is: x1<-rnorm(10) x2<-1+rnorm(10) # Now create a dataframe for lme myDat <- data.frame(c(x1,x2), c(rep("x1", 10), rep("x2", 10)), rep(paste("S", seq(1,10), sep=""), 2)) na ...
written 16 months ago by wewolski10 • updated 16 months ago by Aaron Lun25k
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... Thank you! [ ] default behaviour strikes again! "Omitting drop = FALSE when subsetting matrices and data frames is one of the most common sources of programming errors. (It will work for your test cases, but then someone will pass in a single column data frame and it will fail in an unexpected and ...
written 22 months ago by wewolski10
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... I have the following code: fit <- lmFit(intmat , designMatrix) tmpfit <- fit[,-1] lmfit.cont <- contrasts.fit(fit[,-1], cont[-1,2]) lmfitebayes <- eBayes(lmfit.cont)​ topTable(lmfitebayes, coef=name, number=Inf) Which fails when executing topTable sometimes. Thats because contrast. ...
written 22 months ago by wewolski10 • updated 22 months ago by Aaron Lun25k
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... "Is it possible that the expression values have simply failed to meet some detection threshold for this condition?" No, it is not. Let me assure you, I did try to understand and model where the missingness is coming from.  If I used the imputation you suggest I would introduce a heavy bias. Bias is ...
written 2.1 years ago by wewolski10 • updated 2.1 years ago by Gordon Smyth38k
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... Thanks, Gordon, I have now a solution based on the post:  https://support.bioconductor.org/p/19879/ but it is a hack, workaround, and features usually do not need workarounds.  Still, if you think that contrast.fit not handling NA is a feature why not just add contrast.fit.NA to limma which is a ...
written 2.1 years ago by wewolski10 • updated 2.1 years ago by Gordon Smyth38k
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... I will try to describe briefly what I am doing: my design matrix designMatrix <- model.matrix( ~ 0 + Condition + Plant, data=grp2$annotation_) > unique(grp2$annotation_\$Condition) [1] "PC_16h_sys"  "PC_16h_test" "PC_38h_sys"  "PC_38h_test" "PC_96h_sys"  "PC_96h_test" Then I define the con ...
written 2.1 years ago by wewolski10 • updated 2.1 years ago by Gordon Smyth38k
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... Hi, Just comparing the output of limma and lme. The model that I fit with lme is : le <- lme(lmIntensity ~ Condition, random = ~1|Donor, data = x) Since I have repeated measures (Condition) on the same Donor and I am not interested in the Donor effect I model it as random effect. In lim ...
written 2.4 years ago by wewolski10 • updated 2.4 years ago by Aaron Lun25k

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