User: LJ

gravatar for LJ
LJ210
Reputation:
210
Status:
Trusted
Location:
Last seen:
2 years, 11 months ago
Joined:
3 years, 10 months ago
Email:
j*************@gmail.com

Posts by LJ

<prev • 29 results • page 2 of 3 • next >
1
vote
1
answer
2.6k
views
1
answer
what is the meaning of covariates in ComBat
... Can anyone tell me what the difference between the following code1 and code2 is? code1: pheno<-read.table(file="pdata.txt",header=T,row.names=1) head(d) subgroups batch sample1 1 1 sample2 1 1 sample3 1 1 sample4 ...
R combat written 3.8 years ago by LJ210
2
votes
1
answer
14k
views
1
answers
Comment: C: removing batch effects using ComBat and SVA
... ok,but i just saw a explanation for Covariates in ComBat [here][1] from Dr.Johnson (the author of "sva" package),it seems that he gave a opposite meaning of covariates, and the following is the answer to the purpose of including covariates in the mode: > Sorry about the late response. However, th ...
written 3.8 years ago by LJ210
0
votes
1
answer
14k
views
1
answers
Comment: C: removing batch effects using ComBat and SVA
... So the code modcombat<-model.matrix(~1, data=pheno) combat_mydata<-ComBat(dat=mydata, batch=batch, mod=modcombat, par.prior=TRUE, prior.plots=FALSE) only removes batch effects but subgroups variation retained. However,when i add a covariate level--subgroups,the following code m ...
written 3.8 years ago by LJ210
1
vote
1
answer
14k
views
1
answers
Comment: C: removing batch effects using ComBat and SVA
... Thanks.One more question for you,and the following code is what i used in ComBat: > pheno subgroups batch sample1 N 1 sample2 N 1 sample3 N 1 sample4 N 1 sample5 T ...
written 3.8 years ago by LJ210
0
votes
2
answers
3.9k
views
2
answers
Comment: A: PCA when the dimensionality is greater than the number of samples in R
... Thank you guys for your replies. ...
written 3.8 years ago by LJ210
0
votes
2
answers
3.9k
views
2
answers
Comment: C: PCA when the dimensionality is greater than the number of samples in R
... for example,n=10,m=1000,so the result returns a 10X10 matrix, and the 10 PCs explains 100% variance, but 10 components is far smaller than 1000 features,is it reasonable? ...
written 3.8 years ago by LJ210
4
votes
2
answers
3.9k
views
2
answers
PCA when the dimensionality is greater than the number of samples in R
... Dear all, i have a dataset(n samples containing m dimensions,and **n﹤m**),and i would like to reduce the dimensionality of this data using PCA method("prcomp" function in R).However,it only returns a n-by-n matrix,So how to perform PCA when the dimensionality is greater than the number of sample ...
R pca written 3.8 years ago by LJ210 • updated 3.8 years ago by Carlo Yague4.9k
0
votes
1
answer
14k
views
1
answers
Comment: C: removing batch effects using ComBat and SVA
... Thanks for your reply. (1)My microarrays data was collected in two experiments,and I do the PCA plot, finding the samples are clustering based on the two experiment batches. So,i just set the batch information as the two experiment batches(1,1,1,...,2,2,2,...),then run the ComBat with the batches ...
written 3.8 years ago by LJ210
12
votes
1
answer
14k
views
1
answer
removing batch effects using ComBat and SVA
... Dear all, I have a problem in processing my microarrays data.And I know how the batch effect is structured,soI would like to remove batch effect using ComBat. But I also want to adjust for unknown sources of noise using sva. Is there a way of combining these two methods? And is it feasible that i r ...
R sva combat batch effect written 3.8 years ago by LJ210 • updated 14 months ago by Agustin Gonzalez-Vicente50
0
votes
3
answers
1.7k
views
3
answers
Comment: C: linear regression for removing the population effects
... Thanks for you reply.Two questions for you : (1)So you mean the author used the residuals from the linear model to represent the protein levels and the residuals were protein levels after removing the population effects ? (2)As you can see in the following code: a<-rnorm(100) b<-rnorm ...
written 3.8 years ago by LJ210

Latest awards to LJ

Popular Question 3.1 years ago, created a question with more than 1,000 views. For removing batch effects using ComBat and SVA
Popular Question 3.3 years ago, created a question with more than 1,000 views. For removing batch effects using ComBat and SVA
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Gaussian mixture model in R

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1280 users visited in the last hour