User: Gilgi

gravatar for Gilgi
Gilgi20
Reputation:
20
Status:
New User
Location:
European Union
Last seen:
8 months, 3 weeks ago
Joined:
3 years, 1 month ago
Email:
g******@gmail.com

Posts by Gilgi

<prev • 31 results • page 1 of 4 • next >
0
votes
1
answers
379
views
1
answers
Comment: C: clusterProfiler compareCluster enrichDAVID
... Thanks a lot. Here is the code: data(gcSample) david <- enrichDAVID(gene = gcSample[["X1"]],                      idType = "ENTREZ_GENE_ID",                      annotation = "GOTERM_BP_FAT",                      david.user = "my_mail") (I have registered in DAVID)   The session crashes with ...
written 8 months ago by Gilgi20
0
votes
1
answers
379
views
1
answers
Comment: C: clusterProfiler compareCluster enrichDAVID
... Thanks a lot! ...
written 8 months ago by Gilgi20
1
vote
1
answer
379
views
1
answer
clusterProfiler compareCluster enrichDAVID
... Hello, I have some questions regarding the use of the clusterProfiler package: 1. In the compare dotplot - which categories are chosen to be shown - are these the top functions that had the lowest p-value in any of the clusters? 2. In the compare dotplot – what is the number in parentheses in the ...
clusterprofiler written 9 months ago by Gilgi20 • updated 9 months ago by Guido Hooiveld2.3k
0
votes
1
answers
418
views
1
answers
Comment: C: DESeq2 for translation efficiency when there are normalization issues
... Thanks a lot for the answers. ...
written 21 months ago by Gilgi20
0
votes
1
answers
418
views
1
answers
Comment: C: DESeq2 for translation efficiency when there are normalization issues
... I thought we must do some normalization in order to compare the samples. If we look at the ratio (ribo/total for treated) / (ribo/total for untreated) and just for example, if the sample ribo - treated has a much larger coverage, we might get biased ratios. Am I wrong? ...
written 21 months ago by Gilgi20
0
votes
1
answers
418
views
1
answers
Comment: A: DESeq2 for translation efficiency when there are normalization issues
... Thanks a lot for the quick reply. I have some questions: 1. I think we must at least normalize each data set (ribo and total) separately  in some way before extracting the interaction from DESeq2 (ideally this would be with DESeq2, but maybe the assumption of the normalization is violated). Am I c ...
written 21 months ago by Gilgi20
1
vote
1
answer
418
views
1
answer
DESeq2 for translation efficiency when there are normalization issues
... Hello, We are designing a ribosome footprint experiment in which we have cells with or without treatment. For the same samples we will have also sequencing of total RNA-Seq. Here are the samples we will have: 1. Cells without treatment - total RNA protocol (TruSeq) 2. Cells without treatment - ribo ...
deseq2 ribosome profiling translation efficiency spikes written 21 months ago by Gilgi20
0
votes
5
answers
735
views
5
answers
Answer: A: Diffbind EdgeR and DESeq2 normalization
... Thanks a lot! ...
written 2.1 years ago by Gilgi20
0
votes
5
answers
735
views
5
answers
Answer: A: Diffbind EdgeR and DESeq2 normalization
... Thank you very much. So if I don't expect lots of changes between the samples, it might be better to set bFullLibrarySize=FALSE right?   ...
written 2.1 years ago by Gilgi20
0
votes
5
answers
735
views
5
answers
Answer: A: Diffbind EdgeR and DESeq2 normalization
... Thanks a lot for your quick reply and for the great package. Regarding the normalized counts - I am referring to the counts that are obtained after calling dba.report() with bCounts=TRUE. I ran DiffBind several times and always for DESeq2 one of the columns has integers. When using DESeq2 normaliza ...
written 2.1 years ago by Gilgi20

Latest awards to Gilgi

Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2: Abnormally skewed distribution of p-values
Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2 - 2 factor design
Popular Question 20 months ago, created a question with more than 1,000 views. For SVA package - for removing batch effect after DESeq - error in ComBat

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 278 users visited in the last hour