User: pokharel.kisun

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Posts by pokharel.kisun

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Comment: C: DESeq2 on two groups
... Thanks for the suggestion.  ...
written 8 months ago by pokharel.kisun0
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Comment: C: DESeq2 on two groups
... Hi Mike, sorry for incomplete post. The study consist two breeds and their F1 (i.e 3 breed groups) and two tissues. The two groups you can see in the PCA is for two tissues. One tissue (E) is more heteregenous than the other (C). Within E, there is high within-group variability. I have updated the p ...
written 8 months ago by pokharel.kisun0
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DESeq2 on two groups
... Hi, I just wanted an honest opinion on whether to include two groups together or analyse separately in DESeq2 (please see the pca plot using the link below). I am inclined towards analysing separately, but I want to hear from the readers. Here, the two groups represent two tissues and within each ...
deseq2 group written 8 months ago by pokharel.kisun0 • updated 8 months ago by Michael Love23k
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Comment: C: Ensembl sheep dataset in biomaRt
... Edit: Now, it's working - I don't know how. ...
written 8 months ago by pokharel.kisun0
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Ensembl sheep dataset in biomaRt
... Hi, I have not been able to load latest sheep datasets using biomaRt. The following is the line of code I used:  ensembl<-useDataset(dataset = "oaries_gene_ensembl", mart = ensembl)   and the following is the error message: Error in checkDataset(dataset = dataset, mart = mart) : The given da ...
biomart ensembl oaries written 8 months ago by pokharel.kisun0 • updated 8 months ago by Mike Smith3.3k
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Comment: C: DESeq2: Error in cleanContrast
... Hi Mike, the later error also had to do with the symbol "-". Once I changed it to MC_FR_MR, it didn't throw any error message.      ...
written 21 months ago by pokharel.kisun0
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DESeq2: Error in cleanContrast
... Hi, I have sample table that looks like below: >head(sampletable) SampleId SampleName Location Tissue 1 FR10_MCRP_374D_S108_L005 FR10MC FR MC 2 FR10_MCRP_374D_S56_L001 FR10MC FR MC 3 FR10_MCRP_374D_S56_L002 FR10MC FR MC 4 FR10_MCRP_37 ...
deseq2 design and contrast matrix written 21 months ago by pokharel.kisun0 • updated 21 months ago by Peter Langfelder1.8k
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Comment: C: differential expression analysis using deseq2
... I will go with first option for now. :)  ...
written 22 months ago by pokharel.kisun0
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Comment: C: differential expression analysis using deseq2
... dds<-DESeqDataSetFromMatrix(countData=geneCounts, colData=sampledata, design = ~Breed+Diet+Breed:Diet) dds<-DESeq(dds, parallel = T) res<-results(dds) res<-lfcShrink(dds, coef = 4, res = res) Error in designAndArgChecker(object, betaPrior) : betaPrior=FALSE should be used for desig ...
written 22 months ago by pokharel.kisun0
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Comment: C: differential expression analysis using deseq2
... Hi Mike,  Has there been any change/update in DESeq2 recently because of which I am unable to set up the contrast I mentioned in my question?  dFS_TX<-results(dds, contrast=list(c("groupFS.F", "groupTX.C"), c("groupFS.C", "groupTX.F"))) It was working fine until about a month ago and suddenly ...
written 22 months ago by pokharel.kisun0

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