User: gtechbio

gtechbio0
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Posts by gtechbio

<prev • 20 results • page 1 of 2 • next >
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... Thanks for reply. I will try using a conda environment then. ...
written 8 weeks ago by gtechbio0
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... 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 ...
written 8 weeks ago by gtechbio0 • updated 8 weeks ago by shepherl ♦♦ 1.4k
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... 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 ...
written 9 weeks ago by gtechbio0
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... 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
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... 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
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... 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 ...
written 10 weeks ago by gtechbio0 • updated 10 weeks ago by Michael Love23k
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... 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
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... 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
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... 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 ...
written 8 months ago by gtechbio0 • updated 7 months ago by Rory Stark2.8k
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... 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

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