User: Michal Okoniewski

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Posts by Michal Okoniewski

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edgeR - one way ANOVA, coef parameter interpretation in glmLRT()
... Hey Mark, A question on one-way ANOVA design with edgeR: I do something like that for 3 groups, so similar case like in the vignette (glm functionality): d <- calcNormFactors(d) d <- estimateCommonDisp(d, verbose=TRUE) d <- estimateTagwiseDisp(d) TS <- factor(cc) design<- mod ...
edger written 6.0 years ago by Michal Okoniewski190 • updated 6.0 years ago by Mark Robinson870
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DESeq estimateDispersion query
... I had the same question this morning - noticed a similar thing, while re-running the analyses with no replicates, those with replicates work OK. Simon Anders has apparently been changing some stuff recently in his functions, so hopefully he can explain us, unless we missed an important update... swi ...
deseq written 7.3 years ago by Michal Okoniewski190
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Answer: A: Sliding window t-test?
... Hi Tim, In the package rnaSeqMap we have implemented (also in C) the Aumann-Lindell algorithm, which is sort of slide-and-join algorithm on two windows across the chromosome and finds the regions even when there are some small gaps. The regions found by A-L are "irreducible" -see the paper on theor ...
written 8.0 years ago by Michal Okoniewski190
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Answer: A: Human Exon array annotation problem.
... Dear Fabrice, This probeset happens to match 3 location in the genome (variants/paralogs of EIF3F on chr2, 11, 21), see http://xmap.picr.man.ac.uk/ The good thing is that it does in a uniform way for all 4 probes - so most likely matches a specific domain for 3 variants of EIF3F gene. Which variant ...
written 8.0 years ago by Michal Okoniewski190
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Answer: A: justPLIER output log scale
... Affy scanner produces values on two bytes 0-2^16, so if you have after the plier summarization values with whole-chip max around 13-15, then you have log2 - and they are used in such way as it is easier to interpret fold changes. Anyway - I think even the creators of plier gave it up and use RMA now ...
written 8.0 years ago by Michal Okoniewski190
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Comment: C: what's really in hgu133plus2.db?
... Hey Tim, I discovered the old chips in XMAP browser yesterday, when I was looking for genes with people using the old arrays... cool "legacy" feature :) Are the hits of HGU133plus2 etc in the xmapcore database by chance too? Cheers, Michal ________________________________________ From: bioconducto ...
written 8.3 years ago by Michal Okoniewski190
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Answer: A: Is there annotation package for Affymetrix Human Exon 1.0 ST Array on bioconduct
... Chances are that there is no such thing :) Use exon.pmcdf from xmap.picr.man.ac.uk and exonmap/xmapcore. If you want gene level summaries - go for Brainarray CDFs. Cheers, Michal ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] ...
written 8.3 years ago by Michal Okoniewski190
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Answer: A: exonmap/xmapcore and splicing.index
... Hi Peter, A quick hack that I use at the moment is using both libraries, do xmapConnect() for exonmap and xmap.connect() for xmapcore and calling explicitely the functions like: xmapcore:::probe.to.hit() or exonmap:::si() As I understand from what the guys from PICR in Manchester are doing it is a ...
written 8.6 years ago by Michal Okoniewski190
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Answer: A: Combining data from runs
... As an alternative to limma in case of batch effect, you may try pamr.batchadjust(), works quite well for me, see also eg: http://www.biomedcentral.com/1755-8794/1/42 Cheers, Michal -----Mensaje original----- De: bioconductor-bounces at stat.math.ethz.ch en nombre de Supriya Munshaw Enviado el: vi ...
written 8.7 years ago by Michal Okoniewski190
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Answer: A: how to do it with biomaRt
... Hello Alex, The trick is that your IDs in the biomaRt filter are neither transcripts nor compatible with "affy_raex_1_0_st_v1". Your IDs are Affy transcript clusters - a bit old way of defining features on the Affy Exon chips, abandoned as far as I know in most of the software, perhaps except Gene ...
written 9.6 years ago by Michal Okoniewski190

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Popular Question 6.0 years ago, created a question with more than 1,000 views. For edgeR - one way ANOVA, coef parameter interpretation in glmLRT()

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