User: o.giannakopoulou

Reputation:
0
Status:
New User
Location:
Last seen:
1 week, 4 days ago
Joined:
2 months ago
Email:
o***************@qmul.ac.uk

Posts by o.giannakopoulou

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answers
76
views
1
answers
Comment: C: champ.DMP phenotypes and covariates
... Thank you again for the really informative reply. Indeed, I have paired data (i.e. data of same patients in two time points). I was thinking that I could overcome that by including the patient_id as a covariate in my model. But as I can see from your reply there is not yet this option in champ.DMP() ...
written 11 days ago by o.giannakopoulou0
0
votes
1
answer
76
views
1
answer
champ.DMP phenotypes and covariates
... Hello,  I'm using ChAMP for the analysis of my DNA methylation data obtained with EPIC. I have samples from a set of participants in two time points. I would like to identify the differentially methylated positions between the two time points. The values of Sample_Group are "first" and "second" (st ...
champ champ.dmp() written 13 days ago by o.giannakopoulou0 • updated 11 days ago by Yuan Tian0
0
votes
1
answers
103
views
1
answers
Comment: C: error with champ.load
... Indeed the problem was with editing the excel file. As you guessed, when I was saving the csv file, after adding Sample_Group information, the Sentrix_ID was changing. I managed to make it work after making sure that Sentrix_ID was in "Numeric" format each time.  Thank you again for the help Best ...
written 13 days ago by o.giannakopoulou0
0
votes
1
answer
103
views
1
answer
error with champ.load
... Hello,  I'm using the champ.load to read and filter my data and it works well. However when I want to proceed with the champ.QC I receive an error because the column "Sample_Group" in the csv file provided is empty.  So I tried to add the information of that column ("first" or "second") and use th ...
champ written 17 days ago by o.giannakopoulou0 • updated 16 days ago by Yuan Tian0
0
votes
1
answers
106
views
1
answers
Comment: C: Effect of inclusion of patientID in the formula
... Thank you again, I really appreciate the help. I have gone through the vignette but I was not sure which model was the most appropriate for the analysis I had in my mind. I'll check DESeq2 more targeted now. Thank you again  ...
written 8 weeks ago by o.giannakopoulou0
0
votes
1
answers
106
views
1
answers
Comment: C: Effect of inclusion of patientID in the formula
... Thank you James for your reply. The example of t-test helped me a lot getting a better idea of the effect of PatientID inclusion in the model. So it's now clear how I should compare the expression of each group (cases/controls) between the two visits.  However, I still have some doubts about the mo ...
written 8 weeks ago by o.giannakopoulou0
1
vote
1
answer
106
views
1
answer
Effect of inclusion of patientID in the formula
... Hello, I am currently using DESeq2 to run some test on a case/control RNA-seq dataset with 2 time-point measurements (i.e. each sample has 2 measurements and is either classified as case or control). Cases and controls are not matched/paired. I have read the tutorial and any other relevant info I ...
deseq2 written 8 weeks ago by o.giannakopoulou0 • updated 8 weeks ago by James W. MacDonald45k

Latest awards to o.giannakopoulou

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 2.2.0
Traffic: 174 users visited in the last hour