User: Marc Saric

gravatar for Marc Saric
Marc Saric70
Reputation:
70
Status:
Trusted
Location:
Last seen:
2 weeks, 6 days ago
Joined:
13 years, 2 months ago
Email:
m*********@gmx.de

Posts by Marc Saric

<prev • 13 results • page 1 of 2 • next >
0
votes
1
answer
166
views
1
answers
Comment: C: DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what
... Hi Wolfgang, Thank you for you advice. I may try this. ...
written 12 weeks ago by Marc Saric70
0
votes
0
answers
119
views
0
answers
Comment: C: Error with ComplexHeatmap. Showing only part of image.
... You should probably post code to reproduce the error including the packages you have loaded and sessioninfo() otherwise it is really hard to guess what might have gone wrong. ...
written 12 weeks ago by Marc Saric70
0
votes
1
answer
166
views
1
answers
Comment: C: DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what
... Thank you for your advice. :-) ...
written 12 weeks ago by Marc Saric70
0
votes
1
answer
166
views
1
answers
Comment: C: DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what
... Thanks for the answer: I would guess, that the general assumption for RNA-seq (or microarray experiments) (i.e. most genes do not change) hold for most of the samples. From what is known about that type of cancer, advanced stages show a high degree of mutations and therefore deregulation of many pa ...
written 12 weeks ago by Marc Saric70
4
votes
1
answer
166
views
1
answer
DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
... Dear forum, I am working on a comparison study involving [TCGA][1] RNA-seq data. What I wanted to do is a comparison of cancer vs normal data using the HTSEQ-count data as downloadable from TCGA GDC portal. I would like to use the vst normalized data for downstream analysis (exploratory clustering ...
normalization deseq2 rna-seq tcga vst written 12 weeks ago by Marc Saric70 • updated 12 weeks ago by Michael Love23k
0
votes
2
answers
356
views
2
answers
Answer: A: How can I install DeSeq2 in Jupyter Notebook?
... If you don't mind adding another layer of complexity, you could give the pre-packaged Jupyter-notebook docker-images from https://github.com/jupyter/docker-stacks a try. I think docker is more or less easy to install on Mac, see https://docs.docker.com/docker-for-mac/ Just customize the [datascienc ...
written 12 weeks ago by Marc Saric70
0
votes
1
answer
347
views
1
answers
Answer: A: Preferred RDBMS
... -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Steven Wanyee wrote: > I want to develop a database for importing and storing FCS data files from > our flow lab, and to then use the db with bioconductor tools. And I was just > curious as to which rdbms seems is preferred. If you want to st ...
written 12.0 years ago by Marc Saric70
0
votes
1
answer
565
views
1
answers
Comment: C: biomaRt manual
... Weiwei Shi wrote: > Thanks, Kasper. But I did use method B and found the vignettes. > However, it seems that one is not written in very detailed. I would propose method d) then: Have a look at the source-code to get a clue what functions/methods are available. This is free open source code, ...
written 12.2 years ago by Marc Saric70
0
votes
1
answer
334
views
1
answers
Answer: A: heatmap_2
... Ron Ophir wrote: > Hi, > One of the features of heatmap is to set Colv or Rowv to NA if I don't > wont to perform clustering on columns or rows respectively. This option > does not exist in heatmap_2. Is there another way to show columns or > rows cluster solely? > Thanks, > R ...
written 12.7 years ago by Marc Saric70
0
votes
1
answer
531
views
1
answers
Answer: A: Compiling RMAGEML 2.5.3 or 2.4.0 under Mac OS X 10.4.5 fails
... Hi list, Sorry for bugging you too early with this, has been a compiler- problem, which could be solved with sudo gcc_select 3.3 afterwards at least the compilation of RMAGEML 2.5.3 worked. I will keep yelling for help if things don't work later on. ;-) Sorry again. -- Bye, Marc Saric ...
written 13.1 years ago by Marc Saric70

Latest awards to Marc Saric

Great Question 12.0 years ago, created a question with more than 5,000 views. For Fine tuning heatmap.2 graphics
Popular Question 12.0 years ago, created a question with more than 1,000 views. For Fine tuning heatmap.2 graphics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 202 users visited in the last hour