User: GFM

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GFM20
Reputation:
20
Status:
New User
Location:
European Union
Last seen:
1 week, 1 day ago
Joined:
3 years, 4 months ago
Email:
g******@gmail.com

Posts by GFM

<prev • 33 results • page 1 of 4 • next >
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Comment: C: normalizecoverage in methylkit outputs NAs
... Thank you very much for your answer. I now understand the reason for the problem: since this is short amplicon, and the coverage is quite even in all the CpGs in the amplicon, there are several samples that have no data at all CpGs after the filterByCoverage:  filtered.myobj <- filterByCoverage ...
written 16 days ago by GFM20
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normalizecoverage in methylkit outputs NAs
... Hello, I am using Methylkit for the analysis of bisulfite experiment in amplicons. I am trying to use the normalizeCoverage function, but it transforms the data to NAs. Here is the code: myobj=methRead(file.list,                    sample.id=as.list(paste(as.character(A_B_samples$Sample.2))),       ...
na methylkit normalizecoverage written 21 days ago by GFM20 • updated 21 days ago by altuna akalin20
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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 11 months ago by GFM20
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Comment: C: clusterProfiler compareCluster enrichDAVID
... Thanks a lot! ...
written 11 months ago by GFM20
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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 12 months ago by GFM20 • updated 12 months ago by Guido Hooiveld2.3k
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Comment: C: DESeq2 for translation efficiency when there are normalization issues
... Thanks a lot for the answers. ...
written 2.0 years ago by GFM20
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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 2.0 years ago by GFM20
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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 2.0 years ago by GFM20
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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 2.0 years ago by GFM20
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Answer: A: Diffbind EdgeR and DESeq2 normalization
... Thanks a lot! ...
written 2.3 years ago by GFM20

Latest awards to GFM

Popular Question 23 months ago, created a question with more than 1,000 views. For DESeq2: Abnormally skewed distribution of p-values
Popular Question 23 months ago, created a question with more than 1,000 views. For DESeq2 - 2 factor design
Popular Question 23 months ago, created a question with more than 1,000 views. For SVA package - for removing batch effect after DESeq - error in ComBat

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