User: Adam

gravatar for Adam
Adam20
Reputation:
20
Status:
New User
Location:
Last seen:
7 months, 1 week ago
Joined:
3 years, 3 months ago
Email:
a********@poczta.fm

Posts by Adam

<prev • 24 results • page 1 of 3 • next >
0
votes
0
answers
242
views
0
answers
Healthy controls - samples Illumina 450k methylation
... Hello, I'd like to find some differentialy methylated tags of one particular disease, currently I'm using two databases: https://xena.ucsc.edu/ https://portal.gdc.cancer.gov/ I found whole methylation profile (already normalized data) Beta values of dozens of samples. Nevertheless I can't find a ...
tcga methylation written 7 months ago by Adam20 • updated 7 months ago by Biostar ♦♦ 20
0
votes
0
answers
260
views
0
answers
Comment: C: Two microarray experiments comparison, removing the batch effect
... Actually, all I was needed... https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-335 ...
written 7 months ago by Adam20
0
votes
0
answers
260
views
0
answers
Comment: C: Two microarray experiments comparison, removing the batch effect
... By merging I meant all .CEL files (from two experiments) being normalized together to obtain one expression set that contains all samples. I think that such merging isn't allowed, I'd like to avoid aby bias in my final results. ...
written 7 months ago by Adam20
0
votes
0
answers
260
views
0
answers
Two microarray experiments comparison, removing the batch effect
... Hello, at first, I'd like to mention that smillar questions have been asked several times. However I decided to ask once again because I didin't find satysfying answer, and all present questions are old ~asked over 5 years ago. So could you give me advice, I don't want a ready solution. I have two ...
microarray affymetrix written 7 months ago by Adam20
0
votes
0
answers
271
views
0
answers
Gene symbols - NimbleGen microarray annotation
... Hello, I'd like to make some annotation of methylation microarray by NimbleGen. I have preprocessed data from GEO Let's take this one: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM565262 All I need is gene name/symbol in each row... Unfortunately I didn't find any usefull annotation pac ...
annotation methylation microarray written 8 months ago by Adam20
0
votes
1
answer
360
views
1
answers
Comment: C: Is it possible to get .bed file of sequenced regions after NGS experiment?
... Amazing! That is what I need, many thanks! ...
written 15 months ago by Adam20
2
votes
1
answer
360
views
1
answer
Is it possible to get .bed file of sequenced regions after NGS experiment?
... Hello, As it is in post title, Is it possible to get .bed file of sequenced regions after NGS experiment? I mean that you have results of NGS experiment, let's take WES of 6 samples. Than I'd like to generate .bed file with regions of sequenced regions. To be honest I need this to generate opportu ...
bed ngs written 15 months ago by Adam20 • updated 8 weeks ago by Biostar ♦♦ 20
6
votes
1
answer
993
views
1
answer
How many variants shall I expect in .vcf file?
... **Dear Biologists and Bio-IT-specialists,** based on your knoweledge and experience I'd like to know how many variants should be discovered from .BAM file (final result, after annotation and filtration)? This question is very general, so I'll specify it a bit. Let's take some NGS data (fastq) from ...
vcf ngs written 21 months ago by Adam20 • updated 21 months ago by ATpoint19k
0
votes
1
answer
896
views
1
answers
Comment: C: How to obtain rs ID having genomic position
... Yes I have but the main problem is to compare it into my 'pseudo' BED file ...
written 22 months ago by Adam20
0
votes
1
answer
896
views
1
answers
Comment: C: How to obtain rs ID having genomic position
... Thank you for reply. Yes, I know that it isn't proper BED file and it complicating the problem. Is it possible to convert it into .vcf and then run some variant annotation tools such as SnpSift and SnpEff? ...
written 22 months ago by Adam20

Latest awards to Adam

Popular Question 7 months ago, created a question with more than 1,000 views. For Visualize groups of conditions bys MDS.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 600 users visited in the last hour