User: heikki.sarin

gravatar for heikki.sarin
Reputation:
0
Status:
New User
Location:
Last seen:
4 months ago
Joined:
5 months, 2 weeks ago
Email:
h***********@thl.fi

Posts by heikki.sarin

<prev • 32 results • page 1 of 4 • next >
0
votes
1
answers
378
views
1
answers
Comment: C: DESeq2 model - How to test case/control time course model when taking account wi
... Can you explain why is that compared to the model where condition is also included? Why there isn't need for replicates per sample in that model? ~condition + time + condition:subject.nested + condition:time   ...
written 4 months ago by heikki.sarin0
0
votes
1
answers
467
views
1
answers
Comment: C: DESeq2: How to manually perform filtering and outlier detection?
... Yeah the former is my focus here. 1) I think one of the problems is that I used LRT-test. Do understand correctly that with LRT the "cooks distance" is not applied in the analysis? I have studied the "Cooks distance"-values but I'm not quite sure what threshold to use with manual filtering - they r ...
written 4 months ago by heikki.sarin0
0
votes
1
answers
378
views
1
answers
Comment: C: DESeq2 model - How to test case/control time course model when taking account wi
... Actually I have three timepoints for every subject and almost twenty biological replicates. Shouldn't it work? ...
written 4 months ago by heikki.sarin0
0
votes
1
answers
378
views
1
answers
Comment: C: DESeq2 model - How to test case/control time course model when taking account wi
... That's exactly what I was looking for. However, DESeq2 produces the following error : Warning message: In checkForExperimentalReplicates(object, modelMatrix) :   same number of samples and coefficients to fit,   estimating dispersion by treating samples as replicates.   read the ?DESeq section on ' ...
written 4 months ago by heikki.sarin0
0
votes
1
answers
378
views
1
answers
Comment: C: DESeq2 model - How to test case/control time course model when taking account wi
... Follow-up on this post. If I'd like to perform just case-only analysis with LRT between time-points would the correct models be: ~ subject.nested + time:subject.nested ~ subject.nested So that the between subject variability is taken into account. ...
written 4 months ago by heikki.sarin0
1
vote
1
answer
467
views
1
answer
DESeq2: How to manually perform filtering and outlier detection?
... Hi, I'm quite sure I have a problem with the DESeq2 independent filtering. DESeq2 doesn't flag any outliers when performing the DE analysis. We have little concern about blood being in the samples as the raw counts vary from hundreds to tens of thousands in some HB related genes. For some reason DE ...
deseq2 outliers filtering count outliers written 4 months ago by heikki.sarin0 • updated 4 months ago by Wolfgang Huber13k
0
votes
1
answer
452
views
1
answer
RUVseq: How to implement to more complex time-course model?
... We have quite complex model in the analysis and was wondering about the RUVseq argument "k". Should it be set to 1 or how many in this case below (the vignette isn't really helpful in modifying the example code) ? And is the below right way to implement the W_1 in the model of differential expressio ...
deseq2 ruvseq model.matrix confounders written 4 months ago by heikki.sarin0 • updated 4 months ago by davide risso610
0
votes
1
answers
419
views
1
answers
Comment: C: Dealing with (blood) contamination in RNA-seq data
...     Thank you very much for the help. Going to examine both approaches and see if the results make sense. We have quite complex model in the analysis and was wondering about the RUVseq argument "k". Should it be set to 1 or how many in this case below (the vignette isn't really helpful in modifyi ...
written 4 months ago by heikki.sarin0
0
votes
1
answers
419
views
1
answers
Comment: C: Dealing with (blood) contamination in RNA-seq data
... Yeah, that indeed sounds quite bizarre that WBC would express haemoglobin etc gas exchange related genes.  1) If after RUVseq we still have the same results and there isn't any single high-expression samples in these genes do you see it as plausible that then the results might be genuine? 2) Is it ...
written 4 months ago by heikki.sarin0
0
votes
1
answers
419
views
1
answers
Comment: C: Dealing with (blood) contamination in RNA-seq data
... Little follow-up on the topic. We have RNA-seq gene and exon-level data extracted from white blood cells. We have significant hits on various hemoglobin, haemoglobin metabolic processes and gas exchange related genes from the differential expression analysis. Foldchanges are quite small and vary bet ...
written 4 months ago by heikki.sarin0

Latest awards to heikki.sarin

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: 317 users visited in the last hour