User: gtechbio

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Posts by gtechbio

<prev • 22 results • page 1 of 3 • next >
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Comment: C: collapseReplicates changes the order of the original dataframe in DESeq2
... Hi Michael, thanks for clarifying. If I don´t change the order, the results will be the same, right? ...
written 1 day ago by gtechbio0
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collapseReplicates changes the order of the original dataframe in DESeq2
... 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( ...
deseq2 collapsereplicates written 1 day ago by gtechbio0 • updated 1 day ago by Michael Love24k
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Comment: C: using DESeq2 v 1.18 in Bioconductor v. 3.8
... Thanks for reply. I will try using a conda environment then. ...
written 3 months ago by gtechbio0
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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 3 months ago by gtechbio0 • updated 3 months ago by shepherl ♦♦ 1.4k
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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 4 months ago by gtechbio0
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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 4 months ago by gtechbio0
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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 4 months ago by gtechbio0
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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 4 months ago by gtechbio0 • updated 4 months ago by Michael Love24k
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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 9 months ago by gtechbio0
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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 9 months ago by gtechbio0

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