User: A

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A0
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Posts by A

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Preparation of summarizedExperiment for dexSeq
... Hi all,    I am running in to a problem I have not had before and was wondering if somebody might be able to help. I am processing a summarized experiment object for exonic regions to looks for differential exon usage with the dexseq package. Preprocessing before has always worked, however, I have ...
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Comment: C: Duplication of same sample as if two different samples
... Solved! Indeed an invisible space in some of the samples! Thanks again! ...
written 22 days ago by A0
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Comment: C: Duplication of same sample as if two different samples
... Thanks Michael, I will edit from scracth as you suggest and update DESeq2!   Also, I just realised that 'small intestine' is different to 'small intestine ' with a space in the line! Will edit this all and report back if there is a fix for anyone else who might have this problem!   Many thanks ...
written 22 days ago by A0
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Comment: C: Duplication of same sample as if two different samples
... Thank you Michael,    I get the following result:   Small_Intestine...12 Small_Intestine...8   I can only imagine there may be an alteration in the apostrophe, although there is none entered in the metadata sheet...  ...
written 23 days ago by A0
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Comment: C: Duplication of same sample as if two different samples
... Hi Michael,    Thank you for the quick response.    No the points are not separated, they cluster together. The problem is, is that there are two colours assigned for organ as if they are two separate samples even though they are the same. So I have 24 samples in total for the small intestine. I ...
written 23 days ago by A0
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Duplication of same sample as if two different samples
... Hi all,  I really need help for a problem I have come across since I received another batch of RNA-seq data which I have combined with the first batch. Within both batches I have the same organ but different biological replicates... for example, 2 replicates of the lungs in batch 1 and 2 and the th ...
deseq2 written 23 days ago by A0 • updated 23 days ago by Michael Love19k
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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 3 months 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 3 months 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 3 months ago by A0 • updated 3 months ago by James W. MacDonald48k
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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 4 months ago by A0

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