User: Raheleh

gravatar for Raheleh
Raheleh90
Reputation:
90
Status:
Trusted
Location:
Last seen:
3 days, 17 hours ago
Joined:
2 years, 10 months ago
Email:
r**************@yahoo.com

Posts by Raheleh

<prev • 51 results • page 1 of 6 • next >
0
votes
1
answer
838
views
1
answers
Comment: C: Building a predictive model by a list of genes
... I saw your comprehensive post [here][1] about how to build a lasso-penalised model. I did based on your instruction and I got this coefficient for each gene: $`non-Relapse` 46 x 1 sparse Matrix of class "dgCMatrix" 1 (Intercept) 9.97551314 ASPH ...
written 3 days ago by Raheleh90 • updated 3 days ago by genomax71k
0
votes
1
answer
838
views
1
answers
Comment: C: Building a predictive model by a list of genes
... Thank you Kevin. I'll go through that. Could you please what is the reason that I got this warning and how lasso penalty will solve it? ...
written 4 days ago by Raheleh90
0
votes
1
answer
838
views
1
answers
Comment: C: Building a predictive model by a list of genes
... Many thanks @Kevin for taking the time to address my questions. No, I've never used it before. I really appreciate if you help me with that. ...
written 5 days ago by Raheleh90
0
votes
1
answer
838
views
1
answers
Comment: C: Building a predictive model by a list of genes
... Thank you @Kevin! Yes I want to reduce the predictors via stepwise regression as you said. I have 66 samples (46 non-relapse and 20 relapse). These 45 genes are the genes that I got from differential gene expression analysis. I reduced the number of genes to 24 genes, but still get the same warning ...
written 5 days ago by Raheleh90
0
votes
1
answer
838
views
1
answers
Comment: C: Building a predictive model by a list of genes
... Hi @Kevin. Thank you very much for all your helpful answers. I built a combined model for my data null <- glm(Group ~ 1, data = df, family = binomial(link = 'logit')) full <- glm(Group ~ ASPH + ATP5A1 + ATP5G3 + COL24A1 + DCAF10 + DES + DNMT1 + EIF2B2 + ETS2 + FLJ38 ...
written 6 days ago by Raheleh90
0
votes
1
answer
130
views
1
answers
Comment: C: huge difference of expression value of different probes for the same gene. Why?
... Thank you for your reply. I subtracted off the rowMeans from each row and now it is more meaningful. why we should do this? ![enter image description here][1] [1]: https://i.ibb.co/8XL84FM/Park7-Probes-exp-scaled.png ...
written 11 days ago by Raheleh90
0
votes
1
answer
130
views
1
answers
Comment: C: huge difference of expression value of different probes for the same gene. Why?
... Thanks! I followed the instruction but didn't work ...
written 11 days ago by Raheleh90
4
votes
1
answer
130
views
7 follow
1
answer
huge difference of expression value of different probes for the same gene. Why?
... Hi Folks, I ploted a heatmap for all probes of PARK7 gene to see how they are expressing in three different groups of tumor data. I expected that all probes for the same gene show a similar pattern. However, surprisingly I saw they have huge difference expression value. ![enter image description ...
probe id of the same gene written 11 days ago by Raheleh90 • updated 11 days ago by ATpoint22k
0
votes
0
answers
234
views
0
answers
Comment: C: Should the expression data be centered before PCA?
... Hi Kevin. Thanks for the point! I defined it as "not good" because in the first figure the samples from two different groups are not separated from each other as good as in the second figure. Isn't like this? If I am wrong please correct me. Thanks! ...
written 20 days ago by Raheleh90
6
votes
0
answers
234
views
0
answers
Should the expression data be centered before PCA?
... I have expression profile of 27 samples (10 normal, 17 tumors). I did PCA analysis to check the quality of the samples to see them clustered in 2 different groups. I did it in two ways after RMA normalization and log2 transformation. 1. I did it without centring the data and the result showed that t ...
pca expression data centering written 5 weeks ago by Raheleh90

Latest awards to Raheleh

Supporter 8 days ago, voted at least 25 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Student 10 months ago, asked a question with at least 3 up-votes. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 20 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2278 users visited in the last hour