User: panconchoclo

gravatar for panconchoclo
panconchoclo10
Reputation:
10
Status:
New User
Location:
Sweden
Last seen:
1 month ago
Joined:
3 years, 11 months ago
Email:
v****************@gmail.com

Posts by panconchoclo

<prev • 11 results • page 1 of 2 • next >
0
votes
0
answers
166
views
0
answers
Comment: C: Is right normalize metabolomics "counts" by Variance Stabilized Transformation u
... Thank you Kevin I will do that. To avoid repeat exactly the same question there I will dig more in detail on these packages. ...
written 4 weeks ago by panconchoclo10
0
votes
0
answers
166
views
0
answers
Comment: A: Is right normalize metabolomics "counts" by Variance Stabilized Transformation u
... Hi guys thank you for your reply. Kevin I decided by VST because there are Heteroscedasticity. The behaviour of Means vs SD after and before VST transformation in my data is showed. In the plot 1 you will see that there are some metabolites with a lot of variance. After VST the differences are sl ...
written 5 weeks ago by panconchoclo10
0
votes
0
answers
166
views
0
answers
Is right normalize metabolomics "counts" by Variance Stabilized Transformation using VST DESeq2 package function?
... I want to normalize metabolomics 'counts' data by Variance Stabilizing Transformation. In the meantime I already did that by VST function of using DESeq package and this improve in my opinion the clustering between replicates on a PCA plot which make sense for me. However I just wonder if I need act ...
metabolomics R deseq vst written 5 weeks ago by panconchoclo10 • updated 1 day ago by Biostar ♦♦ 20
0
votes
1
answer
732
views
1
answers
Comment: C: RNA-Seq replicates with big differences in medians of VST values
... Thank you so much shunyip for your answer! Filter out the genes with few counts fix the low medians itself in the box plot but just now I realize that remove those genes is unnecessary for the DE analysis because DESeq do that by default by “independent filtering”. https://support.bioconductor.org ...
written 2.1 years ago by panconchoclo10
1
vote
1
answer
732
views
1
answer
RNA-Seq replicates with big differences in medians of VST values
... Hi, I have RNA-Seq data (5 biological replicates) and after the Variance Stabilizing Transformation (VST) normalization I found that few replicates have the medians really low regarding the other samples/replicates (see plot). I used blind dispersion estimation in DESeq2. I did the same in other ti ...
degs deseq2 rna-seq vst written 2.2 years ago by panconchoclo10 • updated 2.2 years ago by shunyip180
0
votes
5
answers
9.8k
views
5
answers
Comment: C: How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway
... I ran the API and worked out pretty well. I did not check yet if I have some K number without a path assigned but apparently this is what I was looking for a while! Thank you very much 5heikki ...
written 3.0 years ago by panconchoclo10
0
votes
5
answers
9.8k
views
5
answers
Comment: C: How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway
... I ll try use KEGG.db. Thanks! ...
written 3.1 years ago by panconchoclo10
0
votes
1
answer
5.2k
views
1
answers
Comment: C: Pvclust:Error In Clustering
... Diana, use r = 1.0 could solve the problem (ordinary bootstrap instead of multiscale bootstrap option). Did you try with a smaller nboot value first? How many memory do you have? ...
written 3.1 years ago by panconchoclo10
0
votes
5
answers
9.8k
views
5
answers
Answer: A: How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway
... I see. Thanks a lot b.nota and Vari for your comments. ...
written 3.1 years ago by panconchoclo10
0
votes
5
answers
9.8k
views
5
answers
Answer: A: How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway
... In my case using the ko00001.keg file does not solve the problem at all because I have some "K numbers" which does not exist in this file. Any idea where a suitable file with all the mappings is available? Thanks!!   ...
written 3.2 years ago by panconchoclo10

Latest awards to panconchoclo

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 2.3.0
Traffic: 1417 users visited in the last hour