User: Gilgi

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Gilgi10
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New User
Location:
European Union
Last seen:
2 weeks, 6 days ago
Joined:
2 years, 5 months ago
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Posts by Gilgi

<prev • 31 results • page 1 of 4 • next >
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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 21 days ago by Gilgi10
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Comment: C: clusterProfiler compareCluster enrichDAVID
... Thanks a lot! ...
written 21 days ago by Gilgi10
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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 25 days ago by Gilgi10 • updated 25 days ago by Guido Hooiveld2.2k
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Comment: C: DESeq2 for translation efficiency when there are normalization issues
... Thanks a lot for the answers. ...
written 13 months ago by Gilgi10
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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 13 months ago by Gilgi10
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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 13 months ago by Gilgi10
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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 13 months ago by Gilgi10
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Answer: A: Diffbind EdgeR and DESeq2 normalization
... Thanks a lot! ...
written 17 months ago by Gilgi10
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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 17 months ago by Gilgi10
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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 17 months ago by Gilgi10

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