## User: gtechbio

gtechbio0
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#### Posts by gtechbio

<prev • 18 results • page 1 of 2 • next >
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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 3 days 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 3 days 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 3 days 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 4 days ago by gtechbio0 • updated 4 days ago by Michael Love22k
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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 5 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 5 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 5 months ago by gtechbio0 • updated 5 months ago by Rory Stark2.7k
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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 10 months ago by gtechbio0
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... Hi Michael, I am sorry for ignorance, but still I don't understand why my example wouldn't work properly: I specify in design formula that there are two conditions (basically parents), and I control for library size and gene length. So basically it will compare condition 1 vs condition 2, and will s ...
written 10 months ago by gtechbio0
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... Dear Michael, Regarding normalization, so thanks a lot, I will try running the code like that. Regarding the count table, so for example SC1 and SU1 are from the same library (as other samples with the same numbers), and I thought my design will compare alt to ref, like you have mentioned, won't i ...
written 10 months ago by gtechbio0

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