User: Marc Saric

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Marc Saric70
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Posts by Marc Saric

<prev • 16 results • page 1 of 2 • next >
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Comment: C: deseq2 correction batch effect without design
... https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-still-batches-in-the-pca-plot ...
written 8 weeks ago by Marc Saric70
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Comment: C: Scan error using biomart getBM with version option and host set
... Hi Mike, thank you very much. I did that. The error persists today, using `ENSEMBL_DB_HOST = "www.ensembl.org` so you were right and I scaned through the gene ids to provide a minimum example to better reproduce the failure: The culprit was go_sets <- getBM(attributes = c("ensembl_gene_ ...
written 5 months ago by Marc Saric70
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Scan error using biomart getBM with version option and host set
... Dear all, I ran the following code and hit the error already described in https://support.bioconductor.org/p/104454/, https://support.bioconductor.org/p/104845/, and https://support.bioconductor.org/p/106479/. Additional note: The main EnsEMBL BioMart seems to be down for maintenance currently, so ...
biomart ensembl getbm written 6 months ago by Marc Saric70
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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 8 months ago by Marc Saric70
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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 8 months ago by Marc Saric70
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Comment: C: DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what
... Thank you for your advice. :-) ...
written 9 months ago by Marc Saric70
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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 9 months ago by Marc Saric70
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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 9 months ago by Marc Saric70 • updated 9 months ago by Michael Love26k
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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 9 months ago by Marc Saric70
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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 12.5 years ago by Marc Saric70

Latest awards to Marc Saric

Epic Question 12.5 years ago, created a question with more than 10,000 views. For Fine tuning heatmap.2 graphics
Great Question 12.5 years ago, created a question with more than 5,000 views. For Fine tuning heatmap.2 graphics
Popular Question 12.5 years ago, created a question with more than 1,000 views. For Fine tuning heatmap.2 graphics

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