User: lawarde.ankita1

Reputation:
20
Status:
New User
Location:
Last seen:
7 months, 3 weeks ago
Joined:
10 months, 3 weeks ago
Email:
l**************@gmail.com

Posts by lawarde.ankita1

<prev • 18 results • page 1 of 2 • next >
0
votes
2
answers
482
views
2
answers
Comment: C: Difficulty in finding DEG using TCGA data from FireBrowse
... Hello svlachavas, I'm so sorry that i have misinterpreted the EBSeq usage and making it more confusing. I am very sorry for the inconvenience I caused. Thank you so much for this explanation.  I will try the last part you mentioned in above comment.   Thanks again, Ankita. ...
written 8 months ago by lawarde.ankita120
0
votes
2
answers
482
views
2
answers
Comment: C: Difficulty in finding DEG using TCGA data from FireBrowse
... Hello svlachavas, Aaron Lun, I'm very sorry to disturb you again, but i just wanted to ask this question about EBSeq package, I'm referring to the EBSeq package, so one question i wanted to ask,  1) Can i use RSEM normalized counts as input to the EBSeq pipeline? As this package is especially fo ...
written 8 months ago by lawarde.ankita120
0
votes
2
answers
482
views
2
answers
Comment: C: Difficulty in finding DEG using TCGA data from FireBrowse
... Hi svlachavas,  Thank you very much for the reply and the explanation. But still i have one query about the link you have provided, that link is about analyzing colorectal cancer data. So can i use this R package for my data (for LUAD data) ? I had earlier gone through this link, but thought that ...
written 8 months ago by lawarde.ankita120
0
votes
2
answers
482
views
2
answers
Comment: C: Difficulty in finding DEG using TCGA data from FireBrowse
... Hi Aaron Lun, Thank you for explaining me that point about gene filtering. And today i did not use any filtering strategy and also i did not use voom function and yet there is zero DEG between stage I and stage IV. And you have mentions in your first reply about voomWithQualityWeights and calcNor ...
written 8 months ago by lawarde.ankita120
0
votes
2
answers
482
views
2
answers
Comment: C: Difficulty in finding DEG using TCGA data from FireBrowse
... Hi Efstathios-lason, Yes i tried, I have used TCGA data from GDC portal and i had asked some question in biostars as i wasn't getting any DEG. That time I was grouping samples according to days to death where, less than one year and more than three years was the grouping method. So i changed the da ...
written 8 months ago by lawarde.ankita120
0
votes
2
answers
482
views
2
answers
Comment: C: Difficulty in finding DEG using TCGA data from FireBrowse
... Hi Aaron Lun, Thank out for pointing out wrong steps in my R code.  Referring to your first point, I don't know how to obtain raw counts from FireBrowse. There in the FireBrowse only normalized gene expression data i found. If you know from where i can get the raw counts for the LUAD data please ...
written 8 months ago by lawarde.ankita120
0
votes
2
answers
482
views
2
answers
Comment: C: Difficulty in finding DEG using TCGA data from FireBrowse
... Hello Agaz Hussain Want, Yes did try topTable without setting the p.value and lfc, but then it give all genes as DEG(around 17000 genes). As referring to my question is this the R code correct for this type of data?? Am I following it correctly or is there anything I'm doing wrong in the analysis ...
written 8 months ago by lawarde.ankita120
6
votes
2
answers
482
views
2
answers
Difficulty in finding DEG using TCGA data from FireBrowse
... Hello sir/madam, I am working on LUAD data obtained from FireBrowse. Its a RNSseqV2 RSEM normalized data of gene expression (file name: LUAD.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data, renamed this file to LUAD_RNA_seq) I want to find Differential gene e ...
limma tcga deg firebrowse written 8 months ago by lawarde.ankita120 • updated 8 months ago by svlachavas620
0
votes
1
answers
200
views
1
answers
Comment: C: Error while getFirehoseData of RTCGAToolbox package
... Hi Marcel Ramos, Yes, I have windows OS on my laptop and that is the reason i was getting the error. Thank you so much for the response. Ankita   ...
written 8 months ago by lawarde.ankita120
1
vote
1
answer
200
views
1
answer
Error while getFirehoseData of RTCGAToolbox package
... Hi, I'm using LUAD data from FireBrowse and i was following RTCGAToolbox tutorial (http://genomicsclass.github.io/book/pages/tcga.html) but when try to download the data i'm getting one error, Here is the R code i used , library(RTCGAToolbox) readData = getFirehoseData (dataset="LUAD", runDate=" ...
R rtcgatoolbox firehose getfirehosedata written 8 months ago by lawarde.ankita120 • updated 8 months ago by Marcel Ramos ♦♦ 310

Latest awards to lawarde.ankita1

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: 174 users visited in the last hour