User: A
A • 0
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Posts by A
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... 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
A • 0
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... 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 ...
written 4 weeks ago by
A • 0
• updated 4 weeks ago by
Michael Love ♦ 17k
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... 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 ...
written 8 weeks ago by
A • 0
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... Thank you so much for clarifying!
...
written 11 weeks ago by
A • 0
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... 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 ...
written 11 weeks ago by
A • 0
• updated 11 weeks ago by
Michael Love ♦ 17k
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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
A • 0
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... 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 ...
written 12 weeks ago by
A • 0
• updated 12 weeks ago by
James W. MacDonald ♦ 46k
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... 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
A • 0
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... 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 ...
written 3 months ago by
A • 0
• updated 3 months ago by
Michael Love ♦ 17k
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... Amazing! Thank you so much for making that crystal clear!
...
written 3 months ago by
A • 0
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