User: Vladimir Krasikov

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Posts by Vladimir Krasikov

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Comment: C: Samples without pair in paired design experiment
... Thanks a lot Gordon for clarification of this point. ...
written 11 weeks 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 11 weeks 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 12 weeks ago by Vladimir Krasikov90 • updated 11 weeks ago by Gordon Smyth31k
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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 3 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 3 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 3 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 3 months ago by Vladimir Krasikov90
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Comment: C: arrayQualityMetrics package - bugs and errors
... Dear Wolfgang Thanks a lot for your advises. Bellow I provide error messages for my case On Wed, 15 Feb 2012 19:42:27 +0100, Wolfgang Huber wrote: > Dear Vladimir > > Thank you for the feedback and the detailed descriptions. > > To remove the reason for the warning from KernSmooth ...
written 5.5 years ago by Vladimir Krasikov90
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Answer: A: Limma: questions about data pre-processing
... Dear Axel Anyway thanks a lot for your efforts, and I sorry if that took too much time I will try to communicate with the company to get row and column coordinates, however earlier they refused to provide me with FE files, so chances are low. Regards Vladimir On Wed, 15 Feb 2012 19:31:55 +0100, ...
written 5.5 years ago by Vladimir Krasikov90
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Comment: C: arrayQualityMetrics package - bugs and errors
... Thanks Martin It fixes the installation problem Vladimir On Wed, 15 Feb 2012 15:40:09 +0100, Martin Morgan wrote: > On 02/15/2012 04:44 AM, Vladimir Krasikov wrote: >> Dear list >> >> While trying to analyze my data with arrayQualityMetrics (thanks to >> Axel Klenk fo ...
written 5.5 years ago by Vladimir Krasikov90

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