User: pokharel.kisun

Reputation:
0
Status:
New User
Last seen:
1 year, 2 months ago
Joined:
3 years, 9 months ago
Email:
p*************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by pokharel.kisun

<prev • 15 results • page 1 of 2 • next >
0
votes
1
answer
314
views
1
answers
Comment: C: DESeq2 on two groups
... Thanks for the suggestion.  ...
written 15 months ago by pokharel.kisun0
0
votes
1
answer
314
views
1
answers
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 15 months ago by pokharel.kisun0
2
votes
1
answer
314
views
1
answer
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 15 months ago by pokharel.kisun0 • updated 15 months ago by Michael Love26k
0
votes
1
answer
276
views
1
answers
Comment: C: Ensembl sheep dataset in biomaRt
... Edit: Now, it's working - I don't know how. ...
written 15 months ago by pokharel.kisun0
2
votes
1
answer
276
views
1
answer
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 15 months ago by pokharel.kisun0 • updated 15 months ago by Mike Smith4.0k
0
votes
2
answers
1.2k
views
2
answers
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 2.4 years ago by pokharel.kisun0
4
votes
2
answers
1.2k
views
2
answers
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 2.4 years ago by pokharel.kisun0 • updated 2.4 years ago by Peter Langfelder2.3k
0
votes
1
answer
1.1k
views
1
answers
Comment: C: differential expression analysis using deseq2
... I will go with first option for now. :)  ...
written 2.5 years ago by pokharel.kisun0
0
votes
1
answer
1.1k
views
1
answers
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 2.5 years ago by pokharel.kisun0
0
votes
1
answer
1.1k
views
1
answers
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 2.5 years ago by pokharel.kisun0

Latest awards to pokharel.kisun

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 289 users visited in the last hour