User: deathmagnetic20
deathmagnetic20 • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- ISPA
- Last seen:
- 1 month, 1 week ago
- Joined:
- 9 months, 1 week ago
- Email:
- d**************@gmail.com
Posts by deathmagnetic20
<prev
• 10 results •
page 1 of 1 •
next >
0
votes
0
answers
118
views
0
answers
... I have filtered in R a Illumina Human Methylation 450K data into a data frame of my cg's of interest. Look like this:
head(x_filtered[1:3])
TCGA-WB-A81T-01A TCGA-WB-A81G-01A TCGA-WB-A815-01A
cg12150457 0.12335296 0.10067159 0.13113157
cg07035961 ...
written 7 weeks ago by
deathmagnetic20 • 10
0
votes
1
answer
166
views
1
answers
... Yes with my low code level, sorry!
I meant I dont know how to include all the barcodes and cell types but manually. ...
written 8 weeks ago by
deathmagnetic20 • 10
0
votes
1
answer
166
views
1
answers
... I will try it, thanks!
Challenging, cause I have to include 178 rows (barcodes) and 28 (cell types). Is there a simple code to do it? ...
written 8 weeks ago by
deathmagnetic20 • 10
0
votes
1
answer
166
views
1
answers
... Thank you!
My problem is that I have a table data format like this one, so I dont know how to reorder in order to have the columns you said:
![enter image description here][1]
[1]: https://i.ibb.co/7VS9WPs/Captura-de-pantalla-2020-11-26-a-las-21-18-22.png ...
written 8 weeks ago by
deathmagnetic20 • 10
0
votes
1
answer
166
views
1
answers
... Reposted the image, sorry! ...
written 8 weeks ago by
deathmagnetic20 • 10
3
votes
1
answer
166
views
1
answer
... Hi,
I have used the analytical tool CIBERSORTx to impute gene expression profiles and provide an estimation of the abundances of member cell types in a mixed cell population, using RNAseq and TCGA data. The output table have TCGA barcodes in rows, and cell types in columns. I would like to generate ...
written 8 weeks ago by
deathmagnetic20 • 10
• updated
8 weeks ago by
bioinformatics2020 • 570
1
vote
1
answer
396
views
1
answers
... I agree. The problem is that scaling per gene extremely stratify the samples (after create an event vector) over the median expression gene of interest value, so almost the entire samples are "high expression". I'm not completely sure if global z-score is a bad practice for survival analysis with g ...
written 9 months ago by
deathmagnetic20 • 10
0
votes
1
answer
396
views
1
answers
... Thank you very much Kevin, your reply has been very helpful to me.
I have been doing some research and I still don't know why one approach would be more favorable rather than the other one.
Scaling by row shows me very low expression values, so I tried by global and I get a median z-score of my ge ...
written 9 months ago by
deathmagnetic20 • 10
3
votes
1
answer
396
views
1
answer
... Hi Biostars community,
I am currently doing survival and other analyses in RNAseq gene expression data using the ACC TCGA database.
How can i change the code for obtaining the z-score applying this formula?
> z = [(value gene X in tumor Y)-(mean gene X in tumor)]/(standard
> deviation X in ...
written 9 months ago by
deathmagnetic20 • 10
• updated
9 months ago by
Kevin Blighe ♦ 69k
0
votes
1
answer
65k
views
1
answers
... Hi TriS and community,
Thank you so much for this tutorial, it is being extremely helpful and insightful to me. How can i change the code for obtaining the z-score
scal <- function(x,y){
mean_n <- rowMeans(y) # mean of normal
sd_n <- apply(y,1,sd) # SD of normal
...
written 9 months ago by
deathmagnetic20 • 10
Latest awards to deathmagnetic20
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 970 users visited in the last hour