User: GFM

gravatar for GFM
GFM20
Reputation:
20
Status:
New User
Location:
European Union
Last seen:
2 months, 1 week ago
Joined:
3 years, 10 months ago
Email:
g******@gmail.com

Posts by GFM

<prev • 34 results • page 1 of 4 • next >
0
votes
1
answer
109
views
1
answer
DiffBind with highly variable FRiP (Fraction Reads in Peaks)
... Hello, I am analyzing H3K27Ac ChIP seq samples from paired samples from disease and healthy tissues (each pair from one individual). Peaks were called with MACS2. The number of peaks and the FRiP (fraction of peaks in reads) is very different between the two experimental groups: IP_sample Number_P ...
diffbind written 3 months ago by GFM20 • updated 10 weeks ago by Rory Stark2.8k
0
votes
1
answer
147
views
1
answers
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 6 months ago by GFM20
0
votes
1
answer
147
views
1
answer
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 7 months ago by GFM20 • updated 7 months ago by altuna akalin20
0
votes
1
answer
715
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 18 months ago by GFM20
0
votes
1
answer
715
views
1
answers
Comment: C: clusterProfiler compareCluster enrichDAVID
... Thanks a lot! ...
written 18 months ago by GFM20
1
vote
1
answer
715
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 18 months ago by GFM20 • updated 18 months ago by Guido Hooiveld2.4k
0
votes
1
answer
634
views
1
answers
Comment: C: DESeq2 for translation efficiency when there are normalization issues
... Thanks a lot for the answers. ...
written 2.6 years ago by GFM20
0
votes
1
answer
634
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 2.6 years ago by GFM20
0
votes
1
answer
634
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 2.6 years ago by GFM20
1
vote
1
answer
634
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 2.6 years ago by GFM20

Latest awards to GFM

Popular Question 2.4 years ago, created a question with more than 1,000 views. For DESeq2: Abnormally skewed distribution of p-values
Popular Question 2.4 years ago, created a question with more than 1,000 views. For DESeq2 - 2 factor design
Popular Question 2.4 years 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 16.09
Traffic: 294 users visited in the last hour