## User: gtechbio

gtechbio0
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#### Posts by gtechbio

<prev • 22 results • page 1 of 3 • next >
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... Hi Michael, thanks for clarifying. If I don´t change the order, the results will be the same, right? ...
written 4 months ago by gtechbio0
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... Hi all, I noticed a strange behaviour of collapseReplicates function of DESeq2 v 1.22.2. After collapsing replicates, DESeq2 for some reorders the columns in the dataframe. Below is an example: m <- matrix(sample.int(100, size = 28*100, replace = T), ncol = 28, nrow = 100) rownames( ...
written 4 months ago by gtechbio0 • updated 4 months ago by Michael Love26k
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... Thanks for reply. I will try using a conda environment then. ...
written 8 months 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 months ago by gtechbio0 • updated 8 months ago by shepherl ♦♦ 1.7k
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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 months 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 months 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 months 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 9 months ago by gtechbio0 • updated 9 months ago by Michael Love26k
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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 14 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 14 months ago by gtechbio0

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