User: JackieMe

gravatar for JackieMe
JackieMe0
Reputation:
0
Status:
New User
Location:
Last seen:
2 months ago
Joined:
3 months, 3 weeks ago
Email:
j************@gmail.com

Posts by JackieMe

<prev • 7 results • page 1 of 1 • next >
0
votes
0
answers
106
views
0
answers
Need help determine optimal argument value on a rbsurv model
... I am using the rbsurv packaeg to select surival-assosiated probes. My data was pre-processed microarray data with ~7,000 probes and 192 tumor samples. Data was split in half for modeling and validation(train and test data).  I also included in my model a risk predictor, tumor stage, to help model fi ...
microarray survival rbsurv written 12 weeks ago by JackieMe0
0
votes
1
answers
167
views
1
answers
Comment: C: Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene an
... Thanks! That's exactly what I am looking for. ...
written 3 months ago by JackieMe0
0
votes
1
answers
167
views
1
answers
Comment: C: Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene an
... Thank you Gordon! I am sorry if I am asking some strange questions. In addition to this, multiple mapping ( dual probes mapping to a gene ) is common in hgu133plus array. I've seen some posts online said that to replace the expression values of the probes with thier mean/max expression values.     ...
written 3 months ago by JackieMe0
0
votes
1
answer
167
views
1
answer
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
... I am learning to do differentially expressed gene analysis on microarray data(typically Affaymetrix GeneChip Human Genome U133 Plus 2.0 Array) of tumor vs normal. I've read some tutorials and know the basic steps. But I never saw people talk about when exactly to annotate the probes to gene symbols. ...
microarray limma deg written 3 months ago by JackieMe0 • updated 3 months ago by Gordon Smyth32k
0
votes
1
answers
194
views
1
answers
Comment: C: DESeq2/edgeR DEG analysis data input from TCGA and correation analysis
... Thanks for your reply, Aaron! I saw your answer days ago and realized I haven't understand how edgeR works so I went back reading the edgeR User Guild, took me a while to get a glimpse of the capability and usage of edgeR. To answer your suggestion: Yes, I already filtered low-abundance genes out ...
written 3 months ago by JackieMe0
0
votes
2
answers
169
views
2
answers
Answer: A: How to permanently add custom repositories to BiocLite
... Do you mean a local repo on your own computer? That I don't know, maybe this thread is helpful. In case you mean another Bioconductor website, put the something like following line in your ~/.Rprofile :   options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")   This sets the Bi ...
written 3 months ago by JackieMe0
1
vote
1
answer
194
views
1
answer
DESeq2/edgeR DEG analysis data input from TCGA and correation analysis
... Hello alll. I am a newbie in bioinformatics and still learning. The thing is, I want to do differential expressed gene(DEG) analysis in the TCGA RNA-seq data. DESeq2 and edgeR manuals said they require raw count data as input, so I downloaded STAD.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3 ...
edger tcga written 3 months ago by JackieMe0 • updated 3 months ago by Aaron Lun18k

Latest awards to JackieMe

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: 291 users visited in the last hour