User: bioinfo

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Posts by bioinfo

<prev • 17 results • page 1 of 2 • next >
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Comment: C: DESeq2 log fold change
... Thanks for your answer. I saw your post a long time ago: https://www.biostars.org/p/140976/ So was this changed? ...
written 4 weeks ago by bioinfo0
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DESeq2 log fold change
... Dear DESeq2 developer and colleagues, DESeq2 generates an output table including "log2FoldChange". I have two questions about this value. I. As far as I know, this is a moderated version, not a log2 fold change from the raw count value. But I want to have unmoderated value that can be calculated ...
deseq2 written 4 weeks ago by bioinfo0 • updated 4 weeks ago by Michael Love24k
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DESeq2 then fdrtool
... Hi, I am trying to compare two conditions (WT and KO) across multiple tissues in terms of number of significant genes using DESeq2. Some tissues had good distributions of p-values (0-enriched) but some showed skewed to right where I could adjust using fdrtool. In the case, do I need to apply fdrtoo ...
deseq2 fdrtool written 7 months ago by bioinfo0 • updated 7 months ago by Michael Love24k
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Comment: C: Double nested design in DESeq2
... Thanks for follow-up !! Yes, you are correct that they are different cell lines. However, that's why I used "CellLineSuppressed" in my two designs: (1) Condition + Condition:CellLineSuppressed + Condition:CellLineSuppressed:Replicate + Condition:Library (2) Condition + Condition:CellLineSuppressed + ...
written 7 months ago by bioinfo0
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Comment: C: Double nested design in DESeq2
... Thanks for your answer. By the way, what if the effect of condition is dependent on cell line? there are four cell lines total: two from condition WT and two from condition MT: basically nested sample in the condition. That was why I considered two designs in the question. Could you recommend the de ...
written 8 months ago by bioinfo0
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Comment: C: Double nested design in DESeq2
... Hi Michael, thanks for your answer. I used the following scripts but got warning or error depending on design formula at the creation of deseq object. Can you check? Script 1 generating error deseq2.obj <- DESeqDataSetFromMatrix(countData=fCount, colData=sampleSheet ,design= ~ Library)  mm < ...
written 8 months ago by bioinfo0
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Double nested design in DESeq2
... Hi, I am analyzing RNA-seq data with four factors: Condition (WT and MT), CellLine (2 cell lines in each condition), Replicate (3 replicates in each cell line) and library (paired pull-down and control for a replicate): total 2*2*3*2=24 samples (Table is the below). I would like to find the differen ...
deseq2 written 8 months ago by bioinfo0 • updated 8 months ago by Michael Love24k
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DESeq2 for ChIP-seq
... I have ChIP-seq datasets as the following:     Cell Type Condtion 1 A Input WT 2 A Pulldown WT 3 B Input WT 4 B Pulldown WT 5 C Input MT 6 C Pulldown MT 7 D ...
diffbind deseq2 written 11 months ago by bioinfo0 • updated 11 months ago by Michael Love24k
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Comment: C: DESeq2: possible to compare read counts at single nucleotide level ?
... By the way, when ChIP-seq data is analyzed by DESeq2 for differential binding (for example: diffBind), the region is pre-defined by peak calling software such as MACS. Here, the size of region is variable. If read depth is not good for DESeq2, do you think that small size of region is also not good ...
written 12 months ago by bioinfo0
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Comment: C: DESeq2: possible to compare read counts at single nucleotide level ?
... Thanks for your help !! ...
written 12 months ago by bioinfo0

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