User: rina

gravatar for rina
rina0
Reputation:
0
Status:
New User
Location:
Last seen:
1 month ago
Joined:
1 month, 3 weeks ago
Email:
e**************@gmail.com

Posts by rina

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answers
104
views
1
answers
Comment: C: Gaia not returning results - load_cnv problem
... This didn't seem to work either. I get the same error regarding the start and end index. ...
written 5 weeks ago by rina0
0
votes
1
answers
104
views
1
answers
Comment: C: Gaia not returning results - load_cnv problem
... So this error suggests that there is a problem with the markers themselves and not the structure of one of the two matrices?Segment data and markers are both mapped on hg38, so theoretically they should be consistent, right? Is there something specific that I could upload here so you could get an ov ...
written 5 weeks ago by rina0
0
votes
1
answers
104
views
1
answers
Comment: C: Gaia not returning results - load_cnv problem
... Hi Thanks a lot for your help. I had considered that, but for some reason whenever I change the order ( by: setcolorder(cnvMatrix, c("Sample.Name","Chromosome", "Start", "End", "Num.of.Markers","Aberration"))  I get this error  > cnv_obj <- load_cnv(cnvMatrix, markers_obj, nbsamples) Loadin ...
written 6 weeks ago by rina0
1
vote
1
answer
104
views
1
answer
Gaia not returning results - load_cnv problem
... Hello, I perform CNV analysis using TCGA data and the gaia package. I have followed the reference manual of gaia, compared thoroughly the format of my inputs, but I still do not get any results back. The run_gaia function runs without any problem, but it always returns an empty data frame. Here ar ...
gaia cnv written 6 weeks ago by rina0 • updated 6 weeks ago by Sandro Morganella30
0
votes
1
answers
111
views
1
answers
Comment: C: Adding gene names (or symbols) in my DESeq result
... Not an expert, but I had the same question recently and I did it through >library(fuzzyjoin) >regex_left_join(dataframe, genelist,by=c("IDcol"="transID")) where IDcol is the column containing your IDs in your data frame and transID, the IDs column in your list. Hope that helps! ...
written 7 weeks ago by rina0
0
votes
1
answers
90
views
1
answers
Comment: C: BioMart missing IDs
... That was a great and really helpful answer! I will take your pointers into consideration and try to tweak the workflow in a way that I avoid converting IDs. Much appreciated!  ...
written 7 weeks ago by rina0
2
votes
1
answer
90
views
1
answer
BioMart missing IDs
... Looking at the NAs that came up after mapping Ensembl IDs to Entrez IDs using BioMart, I randomly checked one (ENSG00000018607) and it is linked to an Entrez ID that was yet not found. Any ideas what might be the reason? This is the code I used    mart <- useDataset("hsapiens_gene_ensembl", use ...
biomart ensembl entrez gene identifiers written 7 weeks ago by rina0 • updated 7 weeks ago by James W. MacDonald47k
0
votes
1
answer
196
views
1
answer
Error: vector memory exhausted (limit reached?)
... Hi everyone! I am new to the bioinformatics world and I would much appreciate your help. I am following the TCGA Workflow tutorial and at the Genomic Analysis part, specifically on the CNV analysis I get this error Error: vector memory exhausted (limit reached?), when trying to load the information ...
gaia tcga cnv mac os x tcgabiolinks written 7 weeks ago by rina0 • updated 7 weeks ago by rreck20

Latest awards to rina

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: 306 users visited in the last hour