User: Vladimir Krasikov

Reputation:
90
Status:
Trusted
Location:
Last seen:
3 months ago
Joined:
6 years, 5 months ago
Email:
v***********@gmail.com

Posts by Vladimir Krasikov

<prev • 21 results • page 1 of 3 • next >
0
votes
1
answers
180
views
1
answers
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 4 months ago by Vladimir Krasikov90
0
votes
1
answers
180
views
1
answers
Comment: C: Difficulties with probable batch effect in paired blocked (treatment and placebo
... comment removed ...
written 4 months ago by Vladimir Krasikov90
3
votes
1
answer
180
views
1
answer
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 ...
0
votes
1
answers
234
views
1
answers
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 10 months ago by Vladimir Krasikov90
0
votes
1
answers
234
views
1
answers
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 10 months ago by Vladimir Krasikov90
3
votes
1
answer
234
views
1
answer
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 10 months ago by Vladimir Krasikov90 • updated 10 months ago by Gordon Smyth34k
0
votes
2
answers
513
views
2
answers
Comment: C: Samples without pair in paired design experiment
... Thanks a lot Gordon for clarification of this point. ...
written 13 months ago by Vladimir Krasikov90
0
votes
2
answers
513
views
2
answers
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 13 months ago by Vladimir Krasikov90
4
votes
2
answers
513
views
2
answers
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 13 months ago by Vladimir Krasikov90 • updated 13 months ago by Gordon Smyth34k
0
votes
1
answers
383
views
1
answers
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 14 months ago by Vladimir Krasikov90

Latest awards to Vladimir Krasikov

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 215 users visited in the last hour