User: A

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A0
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Comment: C: Results counts post DESeq same raw counts
... Hi Michael,  Many thanks for your reply! Yes I was aware of this, however, this would still mean that, although a significant gene list is identified, as normalized counts are not stored, I wouldn't be able to use the raw count matrix to see for example, how genes change over time as this would not ...
written 4 weeks ago by A0
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Results counts post DESeq same raw counts
... Hi all,  I was just wondering if somebody could help me regarding normalized count after DESeq. I carry out a DESeq on a time course experiment in order to then make a count matrix of significantly expressed genes to look for patterns in gene expression across different samples. However, I have no ...
deseq2 results written 4 weeks ago by A0 • updated 4 weeks ago by Michael Love17k
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Metadata sheet for DEXSeq analysis
... Hi all,  Just wondering if  anybody can offer some help. I have searched for this answer but unfortunately have not found any solutions I am currently looking at an aging population of a specific cell type in various organs and am interested in looking for differential isoform usage over time.  I ...
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Comment: C: Interpretation of results names after LRT
... Thank you so much for clarifying! ...
written 11 weeks ago by A0
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Interpretation of results names after LRT
... Hi all,  Just a quick question regarding a time point experiment I have done.  Having asked quite a few questions and read threads I think I have the right design and statistical test for looking for genes that change over time, however, I would just like confirmation if anybody can clarify, what t ...
deseq2 lrt multiple time points written 11 weeks ago by A0 • updated 11 weeks ago by Michael Love17k
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Comment: C: Error in DESeq "object" not found
... I'd like the term of interest Organ removed though... So it should recognise that I am trying to do this.. Especially as it does in the full model design for the first function? ...
written 12 weeks ago by A0
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Error in DESeq "object" not found
... Hi all,    Any help would be much appreciated. I have searched for this error and cannot find it anywhere but whats more weird is that I have never experienced this before.  I have run the following code: dds<-DESeqDataSetFromMatrix(countData = countdata, colData = sampledata, design = ~ Time ...
deseq2 lrt reduced model written 12 weeks ago by A0 • updated 12 weeks ago by James W. MacDonald46k
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Comment: C: Filtering genes with a minimum number of counts between samples
... Thank you for the reply! I will look into setting a minimum fold change but will also look at defining this using a base r function with the count matrix after DESeq. Thanks once again :) ...
written 3 months ago by A0
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Filtering genes with a minimum number of counts between samples
... Hi all,  I have searched for this high and low with no luck. I was wondering if it is possible (over a time course experiment) to filter genes that have a specific change across the time points.  So for example, I would like to be able to look at genes that change from one time point to another on ...
deseq2 filtering written 3 months ago by A0 • updated 3 months ago by Michael Love17k
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Comment: C: Filtering for genes >100 counts after LRT still showing significant genes with g
... Amazing! Thank you so much for making that crystal clear!    ...
written 3 months ago by A0

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