User: Vladimir Krasikov

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Posts by Vladimir Krasikov

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RNAseq scater error in plotQC()
... Dear creators/maintainers of the scater package First of all, thanks for slim and intuitive package for the scRNAseq data It is my first go with scRNAseq data and I try to follow scater vignettes   Looks like there might be a little bug in plotQC() It happened that  my SingleCellExperiment obje ...
scater scrnaseq plotqc written 5 months ago by Vladimir Krasikov90 • updated 5 months ago by Aaron Lun22k
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Comment: C: Difficulties with probable batch effect in paired blocked (treatment and placebo
... Thanks, Aaron for the fast comments. Is it true that this approach of including Batch effect into the model is most correct one? design1 <- model.matrix(~ Batch0 + Batch0 : Donor.n + Batch0 : Week, Exp.Design) Should not Batch be on the intercept place, and should I use Donor.n (nested within B ...
written 10 months ago by Vladimir Krasikov90
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Comment: C: Difficulties with probable batch effect in paired blocked (treatment and placebo
... comment removed ...
written 10 months ago by Vladimir Krasikov90
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Difficulties with probable batch effect in paired blocked (treatment and placebo) experiment
... Dear Bioconductor Experts. I have RNAseq data with somewhat difficult experimental design and need advice how to deal with it. Briefly, there are 10 paired samples before and after treatment.Samples are derived from human beings with some disorder which were participating in proof of concept clini ...
limma edger deseq2 batch effect paired design written 10 months ago by Vladimir Krasikov90
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Comment: C: Examples of concise description of NGS and bioinformatics (with DESEq2 or edgeR)
... After a full day of searching I am still not able to find any good experimental papers which utilise the DESeq2 workflow in couple of concise paragraphs. ...
written 16 months ago by Vladimir Krasikov90
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Comment: C: Examples of concise description of NGS and bioinformatics (with DESEq2 or edgeR)
... Thank you, Gordon. I should come to idea to have a look myself for the papers where you or Michael Love are coauthors. ...
written 16 months ago by Vladimir Krasikov90
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Examples of concise description of NGS and bioinformatics (with DESEq2 or edgeR) in M&M of biological paper
... Dear Experts, I wonder if somebody contributed to or met biological! paper, where NGS and following bioinformatics are just one of the many methods used, and thus bioinformatics part is described in few concise paragraphs readable by biologists, but understandable by bioinformaticians. Preferably r ...
edger deseq2 written 16 months ago by Vladimir Krasikov90 • updated 16 months ago by Gordon Smyth36k
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Comment: C: Samples without pair in paired design experiment
... Thanks a lot Gordon for clarification of this point. ...
written 19 months ago by Vladimir Krasikov90
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Comment: C: Samples without pair in paired design experiment
... Michael, thanks a lot for an explanation. However DE genes set slightly differs from running DESeq on complete data set, where not paired samples should be discarded automatically (as Gordon Smyth said below), from the DE genes set I obtained when discard not-paired samples manually from experimenta ...
written 19 months ago by Vladimir Krasikov90
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Samples without pair in paired design experiment
... Dear Experts! I am analyzing RNASeq data of 18 paired samples (before and after treatment) in frame of DESeq2 pipeline. In the set some of the pairs are not complete by technical reasons. I am using straightforward design : model.matrix(~ Ind +Treatment, Exp.Design) ... So the question is should ...
deseq2 paired samples written 19 months ago by Vladimir Krasikov90 • updated 19 months ago by Gordon Smyth36k

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Popular Question 4 months ago, created a question with more than 1,000 views. For Limma: questions about data pre-processing

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