User: marco.trizzino83

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Posts by marco.trizzino83

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Comment: C: accounting for technical variation in DESEQ2
... Thank you both for the replies, I'll check what you suggested and let you know if I have more questions. ...
written 14 months ago by marco.trizzino8310
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Comment: C: accounting for technical variation in DESEQ2
... Thanks. So you would recommend performing variance-stabilization before looking for DE genes (or differentially accessible ATAC-seq regions) if I am concern about technical variation? ...
written 14 months ago by marco.trizzino8310
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accounting for technical variation in DESEQ2
... I have a question about DESEQ2 data normalization.  I know that DESEQ2  requires raw reads counts, that the softwares normalizes by seq depth.    But what if I want to account for technical variation? Normally, I would quantile-normalize the data, but I understand that DESEQ2 does not support quan ...
normalization deseq2 written 14 months ago by marco.trizzino8310 • updated 14 months ago by Peter Langfelder2.2k
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Comment: C: Covariates in DESeq2 for Polysome profiling Data
... Will do, thanks so much Mike for being so helpful! ...
written 3.6 years ago by marco.trizzino8310
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Comment: C: Covariates in DESeq2 for Polysome profiling Data
... So, I re-coded it as you suggested, but while when I have only two conditions the results look good and are comparable with the numbers that I got in previous analysis without the input, when instead I have more than two conditions (6) the results are weird: whatever is the pairwise comparison that ...
written 3.6 years ago by marco.trizzino8310
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Comment: C: Covariates in DESeq2 for Polysome profiling Data
... Thanks Mike! Now it works if I only have two conditions. But when I have more than two (6) it doesn't. So, I grouped condition and assay as you recommended in another thread, coding like this: dds <- DESeqDataSetFromMatrix(countData = Nreads, colData=colData_all, design= ~condition) dds$group & ...
written 3.6 years ago by marco.trizzino8310
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Answer: A: Covariates in DESeq2 for Polysome profiling Data
... So, coding it like that (Nreads is the boud matrix): colData=colData_HS_other design(dds) = ~ assay + condition + assay:condition dds <- DESeq( Nreads, test = "LRT", reduced = ~ assay + condition)   I have these two errors: Error in design(dds) = ~assay + condition + assay:condition :    ob ...
written 3.6 years ago by marco.trizzino8310
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Answer: A: Covariates in DESeq2 for Polysome profiling Data
... Thanks Mike!     ...
written 3.6 years ago by marco.trizzino8310
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Answer: A: Covariates in DESeq2 for Polysome profiling Data
... Hi Mike, So, I guess assay1 (IP) and assay2 (INPUT) need to be two different matrix. At this point I am not sure of how to code it. This is how I was coding it without considering input: dds <- DESeqDataSetFromMatrix(countData = IP_reads, colData=colData, design= ~condition) Should I do someth ...
written 3.6 years ago by marco.trizzino8310

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