User: A

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A0
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Posts by A

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Comment: C: venDiagram after limma showing more genes after specifying up or down regulated
... Many thanks! and sorry for the delay in replying. Yes this makes sense. Thank you for helping shed light! ...
written 5 weeks ago by A0
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Comment: C: venDiagram after limma showing more genes after specifying up or down regulated
... Thank you! In response to your first paragraph, does this then imply that the total number of genes in the venn diagram should be the same? but that genes fall in and out of intersections based on whether you specify up or down? Because when I specify up or down, the total number of genes in the ent ...
written 5 weeks ago by A0
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venDiagram after limma showing more genes after specifying up or down regulated specifically
... Hi all,    was wondering if somebody could explain how limma produces genes that will be entered in to a venndiagram. I have produced a vennDiagram using limma results: ebayesliversamples<-eBayes(contrastfitliversamples)....... resultsvennliversamples <- decideTests(ebayesliversamples, met ...
microarray limma venn diagram differential expression venndiagram written 5 weeks ago by A0 • updated 5 weeks ago by James W. MacDonald47k
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Comment: C: DEXSeq time course design
... Hi Alejandro,  Thank you so much for your help above! These models have helped tremendously! They all work perfectly. I was wondering if I could ask a few follow up questions: Is there a way in estimateexonfoldchanges function to to specify both "condition" and "organ" in order to be able to plot ...
written 9 weeks ago by A0
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Comment: C: DEXSeq time course design
... Awesome! Running those 3 formulae right now and will report. Thank you so much once again! and yes, the title 'sample' was indeed included after te DEXSeq object had been created, I just wasn't sure that I had to include it!   Fingers crossed :) have a great day ...
written 9 weeks ago by A0
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Comment: C: DEXSeq time course design
... Hi Alejandro,    Thank you so much for the quick reply! Really appreciate this. Will test these out. A few quick follow up questions: When you write 'sample' in your design formulae, may I ask what you are referring to? The sampledata I have are age and organ (7 organs in total) 4 ages. I would l ...
written 9 weeks ago by A0
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DEXSeq time course design
... Hi all,    Was wondering if somebody could help me with an issue I am having with DEXSeq. The issue is that I am getting basically 100,s of thousands of exons being deferentially used in a time course experiment I am carrying out and was wondering if somebody that has experience with this could he ...
dexseq differential exon usage written 10 weeks ago by A0 • updated 9 weeks ago by Alejandro Reyes1.6k
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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 3 months 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 3 months ago by A0 • updated 3 months ago by Michael Love19k
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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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