User: jgarces

gravatar for jgarces
jgarces10
Reputation:
10
Status:
New User
Location:
Spain
Website:
https://github.com/jga...
Last seen:
3 weeks, 5 days ago
Joined:
1 year, 5 months ago
Email:
j******@unav.es

Posts by jgarces

<prev • 18 results • page 1 of 2 • next >
0
votes
1
answer
2.5k
views
1
answers
Comment: C: PyClone without copy number data
... Hi @fongchunchan. I'm trying to extract minor and mayor cn info from sciClone but I'm not able to differentiate that value correspond to each one because this R package only give me an unique value of cn not two, could you help me? chr st 799_D.ref 799_D.var 799_D.vaf 799_D.cn 799_D. ...
written 5 weeks ago by jgarces10
0
votes
0
answers
80
views
0
answers
Activator o repressor protein in a pathway
... Hi there, Maybe it's a very basic question but I've surfed the (almost entire) web without any success... Once you've performed an functional enrichment (either ORA or GSEA) and detected key GOs or pathways implied in your disease, how can you know if a specific gene within a specific GO has a act ...
pathway written 9 weeks ago by jgarces10
1
vote
1
answer
102
views
1
answers
Comment: C: GISTIC2, some missing samples during the process
... Hi Kevin, you're right with the defaults parameters... I missed the `-maxseg` one and some samples had more segments that the default value. Sorry for this silly error. Thanks a lot! ...
written 3 months ago by jgarces10
1
vote
1
answer
102
views
1
answer
GISTIC2, some missing samples during the process
... Hi everyone, I'm running GISTIC2 (the version 2.0.23, through commands) with some samples present in my SEG file that dissapear totally in the final object (*all_lesions.conf_90.txt*). During the process, it appears the following warning: *"Shortened 234569 segments in 'filePath' that overlap by on ...
gistic2 written 3 months ago by jgarces10
0
votes
1
answer
320
views
1
answers
Answer: A: Rawcopy copy number analysis
... Hi Moritz, I'll try to answer you with my (little) experience with `rawcopy` (and after some emails with the package's author, he's very kind): - The correct output, I guess you mean the segmentation output, is the *segments.txt* file (the other ones are for generating the different plots for th ...
written 5 months ago by jgarces10
0
votes
0
answers
269
views
0
answers
Comment: C: CDF file for Cytoscan arrays
... Thanks Kevin. I've downloaded the CDF file from the second link and I've move to the folder with the CELs but errors don't disappear... thanks anyway! ...
written 5 months ago by jgarces10
0
votes
0
answers
269
views
0
answers
CDF file for Cytoscan arrays
... Hi there, I'm trying to read some CEL files from Cytoscan HD arrays with the R package `affy` but I get this (annoying) error: > u <- read.affybatch(filenames = list.files(pattern=".CEL$")) > u Error in getCdfInfo(object) : Could not obtain CDF environment, prob ...
array cystoscan cdf written 5 months ago by jgarces10
0
votes
0
answers
1.3k
views
0
answers
Comment: C: cdf environment for cytoscan hd array
... Hi @arti.pandey69. Only for curiosity... how did you generate the `cychhp.txt` files? Manually through Affymetrix software or by another R package? Thanks a lot! ...
written 6 months ago by jgarces10
0
votes
1
answer
574
views
1
answers
Comment: C: How to find CNV or CN state information from rawcopy output ?
... Hi @lynn_redman, did the package's author answer you? ...
written 6 months ago by jgarces10
0
votes
0
answers
160
views
0
answers
(Closed) Extract genes around chromosomal position
... Hi there, I'm trying to extract the genes that are around a chromosomal position (let's talk about 1Kb up and downstream, for example), i.e.: taking account position chr1:46508903 see those genes that are 1Kb up and down. Does anybody know if there's a software/script/whatever that can help me to ...
genome chromosomal position written 9 months ago by jgarces10

Latest awards to jgarces

Popular Question 9 months ago, created a question with more than 1,000 views. For Why different tSNE plot with Seurat and Monocle if they'r using the same R package?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1324 users visited in the last hour