User: wewolski

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wewolski10
Reputation:
10
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New User
Location:
Zurich
Last seen:
2 weeks, 5 days ago
Joined:
2 years, 1 month ago
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Posts by wewolski

<prev • 5 results • page 1 of 1 • next >
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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 20 days ago by wewolski10 • updated 20 days ago by Gordon Smyth31k
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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 4 weeks ago by wewolski10 • updated 4 weeks ago by Gordon Smyth31k
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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 4 weeks ago by wewolski10 • updated 19 days ago by Gordon Smyth31k
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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 4 months ago by wewolski10 • updated 4 months ago by Aaron Lun16k
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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 9 months ago by wewolski10

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