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Old 05-19-2014, 11:15 AM   #21
GreboGuru
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Continuing on my post above, I am now trying to generate the fold change between treatments corrected by the effect of time. Using the nomenclature from my post above this is the fold change I would like to generate : (Drug.2h/Drug.0h)/(Placebo.2h/Placebo.0h).

If you will remember, DEU was tested for using the following formulae :

formulaFullModel = ˜ sample + exon + treatment:exon + time:exon + treatment:time:exon
formulaReducedModel = ˜ sample + exon + treatment:exon + time:exon

I am now trying to generate the fold changes that occur using the testForDEU() function. However, this command only takes one variable and my model uses two.

In my scenario (see post above for full explanation) I am thinking that the model that needs to be fit in testForDEU() is '~ sample + time*treatment* exon. With the denominator being 'Placebo'

My questions are: is this the right model to use to obtain the desired fold changes?
can this model be used in testForDEU() with some small modifications?
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Old 03-09-2015, 10:25 AM   #22
emanbadr
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I'm using DEXSeq for the analysis of 16 human tissues. I'm trying to identify exons that are differentially expressed in one tissue against all other tissues. I ran the whole pipeline of DEXSeq on all the sample for all tissues. What I understand is when I have exon with differential usage in the results table, that means it is differentially expressed in at least one tissue but I can't determine which one. I also can't determine if it is differentially expressed on more than one tissue, is that right? is there anyway to know such information?
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Old 04-25-2019, 09:00 PM   #23
aniket
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Hi,

I want to conduct DEU analysis for three different tissues of different conditions namely F, LR and LR.
Here I used the code in DEXseq package of R to make sample table and design. The input data is counts.txt file from FeatureCounts Here I used the code

Code:
sampleTable = data.frame(
  row.names = c("F1","F2","LR1","LR2","LV1","LV2"),
  condition = factor(rep(c("F","LR","LV"),each=2)),
  libType = c("paired-end","paired-end","paired-end", "paired-end","paired-end", "paired-end"))

sampleTable

dxd <- DEXSeqDataSet(cc,design=~sample + exon + condition:exon, featureID=as.factor(exon_ids),
                     groupID=as.factor(clusters),sampleData=sampleTable)
but I only get 'exon fold change' in between F and LR, F and LV but I could not get the exon fold change between LV and LR. kindly suggest the solution to get comparision in between all three conditions.

Thank you,

Aniket.
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