User: swaegers.janne

Reputation:
0
Status:
New User
Last seen:
2 years, 9 months ago
Joined:
3 years ago
Email:
s*************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by swaegers.janne

<prev • 18 results • page 1 of 2 • next >
0
votes
1
answer
650
views
1
answers
Comment: C: pcaExplorer error displaying PCA plot
... sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X Mavericks 10.9.5 locale: [1] nl_BE.UTF-8/nl_BE.UTF-8/nl_BE.UTF-8/C/nl_BE.UTF-8/nl_BE.UTF-8 attached base packages: [1] stats4    parallel  stats     graphics  grDevices utils     datasets  m ...
written 2.8 years ago by swaegers.janne0
1
vote
1
answer
650
views
1
answer
pcaExplorer error displaying PCA plot
... Hi everyone, When using pcaExplorer I keep on getting this error when I go to the tab 'Samples View'. The PCA plot is not displayed. I updated ggplot2 and ggrepel but the error stays... Error: GeomLabelRepel was built with an incompatible version of ggproto. Please reinstall the package that provi ...
pca pcaexplorer written 2.8 years ago by swaegers.janne0 • updated 2.8 years ago by Federico Marini120
0
votes
1
answer
546
views
1
answers
Comment: C: How to account for population variation within regions in DESeq2?
... Thanks for the reply. I did both analyses (with and without outlier) again from scratch within the same session and get the exact same results. Without the latN outlier the comparison of the latS samples results in way less filtering...Could this somehow be related to the trick I used to account for ...
written 2.8 years ago by swaegers.janne0
0
votes
1
answer
546
views
1
answers
Comment: C: How to account for population variation within regions in DESeq2?
... loaded via a namespace (and not attached):  [1] nlme_3.1-128         bitops_1.0-6         pbkrtest_0.4-6       gmodels_2.16.2        [5] RColorBrewer_1.1-2   tools_3.3.0          R6_2.2.0             vegan_2.4-1           [9] rpart_4.1-10         Hmisc_3.17-4         DBI_0.5-1            mgcv_1.8-15 ...
written 2.8 years ago by swaegers.janne0
0
votes
1
answer
546
views
1
answers
Comment: C: How to account for population variation within regions in DESeq2?
... Yes, here it is: > sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.9.5 (Mavericks) locale: [1] nl_BE.UTF-8/nl_BE.UTF-8/nl_BE.UTF-8/C/nl_BE.UTF-8/nl_BE.UTF-8 attached base packages: [1] parallel  stats4    stats     graphics  grDevi ...
written 2.8 years ago by swaegers.janne0
0
votes
1
answer
546
views
1
answers
Comment: C: How to account for population variation within regions in DESeq2?
... Hi again, I have a follow-up question. When I remove an outlier sample which is in the latN.treatment24 group, this also influences which and how many DEG I find for the effect of treatment within the latS samples (so for name="latS.treat24"). How is this possible? I also noticed the removal of the ...
written 2.8 years ago by swaegers.janne0
0
votes
3
answers
601
views
3
answers
Comment: C: How to account for population variation within regions in EdgeR?
... Thanks for your reply! Do you have a suggestion on how to pool the data within populations? Just add up the counts? Or would you first do a normalisation procedure? In EdgeR would this mean adding up the rows of the samples within populatons after y <- calcNormFactors(y) ? ...
written 2.9 years ago by swaegers.janne0
0
votes
3
answers
601
views
3
answers
Comment: C: How to account for population variation within regions in EdgeR?
... Allright, thanks! I'm still wondering though: could I also make the dummy variable "pop.nested" (as below) and then make a design like this: design = ~0 +lat + lat:pop.n Would this be a valid alternative for pooling my samples within the populations? sample    pop    lat    trea ...
written 2.9 years ago by swaegers.janne0
0
votes
3
answers
601
views
3
answers
Comment: C: How to account for population variation within regions in EdgeR?
... Sorry, I used the wrong numbers. So using the above-mentioned design, my question is: Can I also compare latN_treatment1 to latS.treatment1 using this design? So compare the gene expression within the treatment 1 between the N and S latitude? How would you go about to test this? Would this involve m ...
written 2.9 years ago by swaegers.janne0
0
votes
3
answers
601
views
3
answers
Comment: C: How to account for population variation within regions in EdgeR?
... Hi, I have another question related to this answer. Can I also compare latN.treat20 to latS.treat20 using this design? So compare the gene expression within the 20 treatment between the N and S latitude? How would you go about to test this? Thanks in advance! ...
written 2.9 years ago by swaegers.janne0

Latest awards to swaegers.janne

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 16.09
Traffic: 250 users visited in the last hour