User: Vladimir Krasikov

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Posts by Vladimir Krasikov

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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 6 weeks 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 6 weeks 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 6 weeks ago by Vladimir Krasikov90 • updated 6 weeks ago by Gordon Smyth32k
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Comment: C: Samples without pair in paired design experiment
... Thanks a lot Gordon for clarification of this point. ...
written 4 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 4 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 4 months ago by Vladimir Krasikov90 • updated 4 months ago by Gordon Smyth32k
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Comment: C: Complicated paired multi factor design
... Now if I want to add to the experiment another compound (Comp3), how can I extract genes responded differently to the Comp2 and Comp3 related to the Comp1 in first Phenotype? ...
written 5 months ago by Vladimir Krasikov90
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Comment: C: Complicated paired multi factor design
... Thanks a lot, this is what I expected ...
written 5 months ago by Vladimir Krasikov90
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Comment: C: Complicated paired multi factor design
... I updated initial post to reflect what comparisons I am interested in ...
written 5 months ago by Vladimir Krasikov90
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Complicated paired multi factor design
... Hello Experts! I encountered somewhat difficult experimental design. Briefly, blood cells from 2 individuals where treated with 2 different compounds (this compounds supposedly have to force cells switch their type from Phen1 to Phen2). Afterwards cells of different phenotypes were physically sepa ...
deseq2 multiple factor design written 5 months ago by Vladimir Krasikov90

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