User: bioinfo

gravatar for bioinfo
bioinfo0
Reputation:
0
Status:
New User
Last seen:
5 months, 2 weeks ago
Joined:
2 years, 1 month ago
Email:
t********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by bioinfo

<prev • 15 results • page 1 of 2 • next >
0
votes
1
answer
132
views
1
answer
DESeq2 then fdrtool
... Hi, I am trying to compare two conditions (WT and KO) across multiple tissues in terms of number of significant genes using DESeq2. Some tissues had good distributions of p-values (0-enriched) but some showed skewed to right where I could adjust using fdrtool. In the case, do I need to apply fdrtoo ...
deseq2 fdrtool written 5 months ago by bioinfo0 • updated 5 months ago by Michael Love23k
0
votes
1
answer
172
views
1
answers
Comment: C: Double nested design in DESeq2
... Thanks for follow-up !! Yes, you are correct that they are different cell lines. However, that's why I used "CellLineSuppressed" in my two designs: (1) Condition + Condition:CellLineSuppressed + Condition:CellLineSuppressed:Replicate + Condition:Library (2) Condition + Condition:CellLineSuppressed + ...
written 5 months ago by bioinfo0
0
votes
1
answer
172
views
1
answers
Comment: C: Double nested design in DESeq2
... Thanks for your answer. By the way, what if the effect of condition is dependent on cell line? there are four cell lines total: two from condition WT and two from condition MT: basically nested sample in the condition. That was why I considered two designs in the question. Could you recommend the de ...
written 6 months ago by bioinfo0
0
votes
1
answer
172
views
1
answers
Comment: C: Double nested design in DESeq2
... Hi Michael, thanks for your answer. I used the following scripts but got warning or error depending on design formula at the creation of deseq object. Can you check? Script 1 generating error deseq2.obj <- DESeqDataSetFromMatrix(countData=fCount, colData=sampleSheet ,design= ~ Library)  mm < ...
written 6 months ago by bioinfo0
0
votes
1
answer
172
views
1
answer
Double nested design in DESeq2
... Hi, I am analyzing RNA-seq data with four factors: Condition (WT and MT), CellLine (2 cell lines in each condition), Replicate (3 replicates in each cell line) and library (paired pull-down and control for a replicate): total 2*2*3*2=24 samples (Table is the below). I would like to find the differen ...
deseq2 written 6 months ago by bioinfo0 • updated 6 months ago by Michael Love23k
1
vote
1
answer
149
views
1
answer
DESeq2 for ChIP-seq
... I have ChIP-seq datasets as the following:     Cell Type Condtion 1 A Input WT 2 A Pulldown WT 3 B Input WT 4 B Pulldown WT 5 C Input MT 6 C Pulldown MT 7 D ...
diffbind deseq2 written 9 months ago by bioinfo0 • updated 9 months ago by Michael Love23k
0
votes
2
answers
234
views
2
answers
Comment: C: DESeq2: possible to compare read counts at single nucleotide level ?
... By the way, when ChIP-seq data is analyzed by DESeq2 for differential binding (for example: diffBind), the region is pre-defined by peak calling software such as MACS. Here, the size of region is variable. If read depth is not good for DESeq2, do you think that small size of region is also not good ...
written 10 months ago by bioinfo0
0
votes
2
answers
234
views
2
answers
Comment: C: DESeq2: possible to compare read counts at single nucleotide level ?
... Thanks for your help !! ...
written 10 months ago by bioinfo0
0
votes
2
answers
249
views
2
answers
Comment: C: Differential ChIP-seq analysis
... Thanks for your answer ! ...
written 10 months ago by bioinfo0
0
votes
2
answers
249
views
2
answers
Comment: C: Differential ChIP-seq analysis
... Thanks for your answer. It is much clearer now to me. By the way, in the website you mentioned, I cannot read math notation in the wrapping up remarks probably due to browser formatting. Can you check it? ...
written 10 months ago by bioinfo0

Latest awards to bioinfo

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 16.09
Traffic: 221 users visited in the last hour