User: Vladimir Krasikov

Reputation:
90
Status:
Trusted
Location:
Last seen:
1 month ago
Joined:
7 years, 10 months ago
Email:
v***********@gmail.com

Posts by Vladimir Krasikov

<prev • 24 results • page 1 of 3 • next >
0
votes
1
answer
191
views
1
answers
Comment: C: Meta-analysis of RNAseq data
... Thanks for the suggestion. Will take a look ...
written 10 months ago by Vladimir Krasikov90
1
vote
1
answer
191
views
1
answer
Meta-analysis of RNAseq data
... Dear Bioconductor experts! I wonder if there any straightforward pipeline for meta-analysis of RNAseq experiments. Any ideas pointing towards suitable packages, websites, papers are appreciated. Is there a way to compare microarray data and RNAseq data. I just want to initiate discussion and furthe ...
rnaseq microarray meta-analysis public data sets written 10 months ago by Vladimir Krasikov90 • updated 10 months ago by alexvpickering110
0
votes
1
answer
295
views
1
answer
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 16 months ago by Vladimir Krasikov90 • updated 16 months ago by Aaron Lun25k
0
votes
1
answer
448
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 21 months ago by Vladimir Krasikov90
0
votes
1
answer
448
views
1
answers
Comment: C: Difficulties with probable batch effect in paired blocked (treatment and placebo
... comment removed ...
written 21 months ago by Vladimir Krasikov90
3
votes
1
answer
448
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 ...
limma edger deseq2 batch effect paired design written 21 months ago by Vladimir Krasikov90
0
votes
1
answer
385
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 2.3 years ago by Vladimir Krasikov90
0
votes
1
answer
385
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 2.3 years ago by Vladimir Krasikov90
3
votes
1
answer
385
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 2.3 years ago by Vladimir Krasikov90 • updated 2.3 years ago by Gordon Smyth39k
0
votes
2
answers
1.1k
views
2
answers
Comment: C: Samples without pair in paired design experiment
... Thanks a lot Gordon for clarification of this point. ...
written 2.5 years ago by Vladimir Krasikov90

Latest awards to Vladimir Krasikov

Supporter 15 months ago, voted at least 25 times.
Popular Question 15 months ago, created a question with more than 1,000 views. For Limma: questions about data pre-processing

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 228 users visited in the last hour