User: valery.sherina

Reputation:
10
Status:
New User
Location:
United States
Last seen:
1 year, 5 months ago
Joined:
3 years, 9 months ago
Email:
v*************@gmail.com

Posts by valery.sherina

<prev • 7 results • page 1 of 1 • next >
0
votes
2
answers
512
views
2
answers
Comment: C: Help running the nondetects::qpcrImpute on my data?
... You said that the data you are using is normalized. I would replace NA with 40, normalize and than perform the imputation. It should speed up the convergence, as the majority of the values you have in the data matrix are in single digits.  ...
written 17 months ago by valery.sherina10
0
votes
2
answers
512
views
2
answers
Comment: C: Help running the nondetects::qpcrImpute on my data?
... Hello Ryan, I checked exprs(yourdata) and found that some of the values are NA. We use maximum possible Ct value as a starting point for the EM algorithm. I put a code snippet of creating a qPCRset object that I used in simulation study, hope this helps. # Ct_nd is a maximum Ct value # nsamp ...
written 17 months ago by valery.sherina10
0
votes
2
answers
512
views
2
answers
Comment: C: Help running the nondetects::qpcrImpute on my data?
... I was able to load the data. We did not work with the data with over 15% of missing data. I suspect there is an estimation problem in limma. I will closely, and get back to you. ...
written 18 months ago by valery.sherina10
1
vote
2
answers
512
views
2
answers
Answer: A: Help running the nondetects::qpcrImpute on my data?
... Dear Ryan, Thank you for your interest in nondetects, and for pointing out the problem. May I ask you to send me the original data matrix. I am having trouble loading into R the qPCRset object you created. Thank you, Valeriia  ...
written 18 months ago by valery.sherina10
0
votes
1
answer
474
views
1
answers
Comment: C: Creating a qPCRset object from a text file
... The package nondetecs requires you to have replicate samples, i.e. treatment (samples 1 - sample 3) vs control (sample 4 - sample 6). In nondetects package the qPCR set object has genes as rows and samples as columns, with replicate information. ...
written 18 months ago by valery.sherina10
0
votes
1
answer
332
views
1
answers
Answer: A: non detects R Package- txt file
... Dear Shaun, Please see https://support.bioconductor.org/p/104878/ Thank you, Valeriia ...
written 18 months ago by valery.sherina10
0
votes
1
answer
474
views
1
answers
Answer: A: Creating a qPCRset object from a text file
... Dear Shaun, Thank you for your interest in nondetects. Similar question was addressed here: https://support.bioconductor.org/p/47369/ You would need to create a qpcr set object yourself. mat <- matrix(rnorm(9*96), ncol = 6, nrow = 96, byrow = FALSE) raw <- new("qPCRset", exprs = mat, featu ...
written 18 months ago by valery.sherina10

Latest awards to valery.sherina

Scholar 3.7 years ago, created an answer that has been accepted. For A: Help running the nondetects::qpcrImpute on my data?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour