## User: wewolski

wewolski10
Reputation:
10
Status:
New User
Location:
Zurich
Last seen:
2 days, 12 hours ago
Joined:
2 years, 11 months ago
Email:
w*******@gmail.com

#### Posts by wewolski

<prev • 8 results • page 1 of 1 • next >
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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 24 days ago by wewolski10 • updated 23 days ago by Aaron Lun19k
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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 6 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 6 months ago by wewolski10 • updated 6 months ago by Aaron Lun19k
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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 9 months ago by wewolski10 • updated 9 months ago by Gordon Smyth33k
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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 10 months ago by wewolski10 • updated 10 months ago by Gordon Smyth33k
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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 10 months ago by wewolski10 • updated 9 months ago by Gordon Smyth33k
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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 13 months ago by wewolski10 • updated 13 months ago by Aaron Lun19k
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... 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 18 months ago by wewolski10

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