User: Smeeta Shrestha

Reputation:
20
Status:
New User
Location:
Last seen:
3 years, 8 months ago
Joined:
5 years, 8 months ago
Email:
s*************@gmail.com

Posts by Smeeta Shrestha

<prev • 10 results • page 1 of 1 • next >
0
votes
3
answers
1.5k
views
3
answers
Answer: A: estimateCellCounts Visualisations - Adjusting Beta Values for Plotting
... Hi Andrew, I have a question. Why are you dropping the intercept in your model.  you design is showing  design <- model.matrix (~0+treatment_arrays+ ..........)  and not  design <- model.matrix(~treatment_arrays + ..........) Since I tried to adjust for blood count in similiar manner, bu ...
written 3.7 years ago by Smeeta Shrestha20
0
votes
0
answers
1.7k
views
0
answers
Comment: C: wilcoxon signed rank test for data frame
... Thank you  ...
written 3.7 years ago by Smeeta Shrestha20
0
votes
3
answers
1.5k
views
3
answers
Answer: A: estimateCellCounts Visualisations - Adjusting Beta Values for Plotting
... Hi  Andrew , Could you please elaborate  1. mAdj.fit <- fitM$coefficients[,-c(1,2)] 2. mAdj <- as.matrix(mAdj.in) - mAdj.fit %*% t(design[,-c(1,2)]) what the  [,-c(1,2)] means in the syntax 1 and 2 above.   If i understand correctly does it mean removing columns 1 and 2 from the ...
written 3.7 years ago by Smeeta Shrestha20
0
votes
2
answers
1.3k
views
2
answers
Answer: A: mt.teststat
... adjusted = mt.rawp2adjp(rawp.test, procedures) ...
written 3.8 years ago by Smeeta Shrestha20
0
votes
2
answers
1.3k
views
2
answers
Comment: C: mt.teststat
... Hi Wolfgang,   Could you please elaborate the earlier email . > teststat <- mt.teststat(compSet, label, test="t", nonpara="n") > rawp <- 2 * (1-pt(abs(teststat)))   Do i need to include a df .  For my study I have 12 pre and 12 post samples. (n=24)   file 1 0 file 2 1 file 3 0 ...
written 3.8 years ago by Smeeta Shrestha20
0
votes
0
answers
1.7k
views
0
answers
wilcoxon signed rank test for data frame
...   Hi ! Could anyone let me know as how I can do a wilcoxon signed rank test for data frames. I saw some people have attempted to explain at the stack flow.  link : http://stackoverflow.com/questions/21271449/how-to-apply-the-wilcox-test-to-a-whole-dataframe-in-r I have a huge data frame of 360, ...
affy wilcoxon signed rank test data frame written 3.8 years ago by Smeeta Shrestha20
0
votes
3
answers
1.5k
views
3
answers
Answer: A: Analyzing paired pre/post data using limma and adjusting for continuous covariat
... Hi Aaron, Thank you for your response.  I will look into this. regards smeeta ...
written 3.8 years ago by Smeeta Shrestha20
0
votes
3
answers
1.5k
views
3
answers
Answer: A: Analyzing paired pre/post data using limma and adjusting for continuous covariat
... Hi Aaron, Thank you so much for the reply. I would like to discuss the points which you have brought out.   Well for the first point brought up. I agree that “Treatment” is same as Sample_Group. So my question there was do I just proceed as per the script 1 or do I need to add a contrast. My o ...
written 3.8 years ago by Smeeta Shrestha20
2
votes
3
answers
1.5k
views
3
answers
Analyzing paired pre/post data using limma and adjusting for continuous covariates
... Hi Ryan and the limma team I am working on 450K methylation data. We have two groups A and B. Each group has two time points (pre and post intervention). At present I would just like to analyse within group A. My data looks like this: Subject ID Group Time point (pre/post) lymph ...
limma covariate pre/post continous written 3.8 years ago by Smeeta Shrestha20
0
votes
2
answers
1.0k
views
2
answers
Answer: A: minfi release 1.8
... Hi Kasper, Could you please let me know how I can export the bumphunter "dmrs" output from the minfi . I managed to use write.table to export the "dmp". Since the file format is different for dmrs, i am not able to use that. Also can I use B=1(default) in the bumphunter function. I would like to ...
written 5.7 years ago by Smeeta Shrestha20

Latest awards to Smeeta Shrestha

Popular Question 3.7 years ago, created a question with more than 1,000 views. For Analyzing paired pre/post data using limma and adjusting for continuous covariates
Popular Question 3.7 years ago, created a question with more than 1,000 views. For wilcoxon signed rank test for data frame

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour