User: wewolski

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wewolski10
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New User
Location:
Zurich
Last seen:
6 months, 4 weeks ago
Joined:
3 years, 8 months ago
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Posts by wewolski

<prev • 8 results • page 1 of 1 • next >
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Getting Significance for second factor (bioreplicate/subject) when using limma.
... 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 ...
limma anova written 9 months ago by wewolski10 • updated 9 months ago by Aaron Lun23k
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Comment: C: limma - contrast.fit returns coefficients without names
... 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 15 months ago by wewolski10
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limma - contrast.fit returns coefficients without names
... 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. ...
limma written 16 months ago by wewolski10 • updated 16 months ago by Aaron Lun23k
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Comment: C: Why does limma contrast.fit produces NA's for all contrast although missing data
... "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 18 months ago by wewolski10 • updated 18 months ago by Gordon Smyth36k
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Comment: A: Why does limma contrast.fit produces NA's for all contrast although missing data
... 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 19 months ago by wewolski10 • updated 19 months ago by Gordon Smyth36k
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Why does limma contrast.fit produces NA's for all contrast although missing data only in one condition?
... 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 ...
limma contrast lmfit missing data makecontrasts written 19 months ago by wewolski10 • updated 18 months ago by Gordon Smyth36k
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limma for Paired Samples vs. lme
... 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 ...
limma linear model paired samples written 22 months ago by wewolski10 • updated 22 months ago by Aaron Lun23k
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Comment: C: matching of AAStringSet vs. another AAStringSet
... Hi Tobi, Here you have a performant and IMHO easier to use solution based on pure CRAN packages seqinr and AhoCorasickTrie. use : seqinr::read.fasta(file = file, as.string = TRUE, seqtype="AA") to read your fasta. then perform the matching with: system.time(res <- AhoCorasickTrie::AhoCorasi ...
written 2.3 years ago by wewolski10

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