User: gtechbio

gravatar for gtechbio
gtechbio0
Reputation:
0
Status:
New User
Last seen:
1 month, 2 weeks ago
Joined:
1 year, 8 months ago
Email:
g*******@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 gtechbio

<prev • 20 results • page 1 of 2 • next >
0
votes
1
answer
94
views
1
answers
Comment: C: using DESeq2 v 1.18 in Bioconductor v. 3.8
... Thanks for reply. I will try using a conda environment then. ...
written 8 weeks ago by gtechbio0
1
vote
1
answer
94
views
1
answer
using DESeq2 v 1.18 in Bioconductor v. 3.8
... How can one use `DESeq2 v. 1.18` from the latest `Bioconductor v. 3.8`? I need to use one package that works reliably only in `Bioconductor 3.8`, but all my previous analysis was done using `DESeq2 v. 1.18`, which is from older Bioconductor release. Thanks ...
deseq2 bioconductor written 8 weeks ago by gtechbio0 • updated 8 weeks ago by shepherl ♦♦ 1.4k
0
votes
0
answers
101
views
0
answers
removing confounding batch efffect with RUVg
... Hi all, I have an RNAseq experiment confounded by batch effect. Its a time-course design with the following setup: time batch 1 0 1 2 0 1 3 1.5 1 4 1.5 1 5 1.5 1 6 3 1 7 3 1 8 3 1 9 3D 2 ...
rnaseq batch effect ruvg written 9 weeks ago by gtechbio0
0
votes
1
answer
120
views
1
answers
Comment: C: Accounting for batch effect in DESseq2
... Thanks for swift reply Michael! Sorry for not explaining properly, but it seems that what I meant is implemented in RUVg package http://bioconductor.org/packages/release/bioc/vignettes/RUVSeq/inst/doc/RUVSeq.pdf (chapter 2.2), which can be coupled with DESeq2. I am wondering if you have any experien ...
written 9 weeks ago by gtechbio0
0
votes
1
answer
120
views
1
answers
Comment: C: Accounting for batch effect in DESseq2
... Hi Michael, Thanks for the reply. If I would have known in advance the genes which are **not** differentially expressed in 3 and 3D compared to 0 (basically genes which are intact to both types of treatment) **without** the batch effect, can I use these genes to somehow infer the the strength of ba ...
written 9 weeks ago by gtechbio0
3
votes
1
answer
120
views
1
answer
Accounting for batch effect in DESseq2
... Dear all, I am having a problem with removing/accounting for the batch effect in my RNAseq experiment using DESeq2. Initially we did 1 big time-course experiment in one batch of human cells growing with fungus. The colData is the following: time 1 0 2 0 3 1.5 ...
deseq2 batch_effect written 10 weeks ago by gtechbio0 • updated 10 weeks ago by Michael Love23k
0
votes
1
answer
256
views
1
answers
Comment: C: DiffBind confuses coordinates of peaks
... Hi Rory, Thanks for reply! I tried using `DataType = DBA_DATA_FRAME`, but the problem persists and I still get contigs with strange coordinates. ...
written 7 months ago by gtechbio0
0
votes
1
answer
256
views
1
answers
Comment: C: DiffBind confuses coordinates of peaks
... Hi Rory, Thanks for reply. I use DiffBind_2.4.8. If you don't mind, I will send the SessionInfo to your email (the forum has character limitations). ...
written 7 months ago by gtechbio0
1
vote
1
answer
256
views
1
answer
DiffBind confuses coordinates of peaks
... Hi All, I'm analyzing ATAC-seq data and use MACS2 for peak calling and DiffBind for occupancy and affinity analysis. In occupancy analysis when I try to find peaks that are unique to one group, it seems that DiffBind confuses the contigs and coordinates of the peaks. For example I get,   SU68 ...
diffbind atacseq written 8 months ago by gtechbio0 • updated 7 months ago by Rory Stark2.8k
0
votes
1
answer
364
views
1
answers
Comment: C: Allele-specific expression with different gene lenghts
... Thanks for elaborating!Now it makes sense for me. And I guess for human data (i.e. patients or any "case-control" study) this "individualized" approach would matter compared to mine. In my case though I analyze yeasts (they are quite homogenous within the culture), so I can in principle assume that ...
written 13 months ago by gtechbio0

Latest awards to gtechbio

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: 174 users visited in the last hour