User: Adam

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Adam10
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2 months ago
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2 years, 10 months ago
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Posts by Adam

<prev • 24 results • page 1 of 3 • next >
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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 11 weeks ago by Adam10 • updated 9 weeks ago by Biostar ♦♦ 20
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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 11 weeks ago by Adam10
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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 11 weeks ago by Adam10
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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 11 weeks ago by Adam10
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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 3 months ago by Adam10
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Comment: C: Is it possible to get .bed file of sequenced regions after NGS experiment?
... Amazing! That is what I need, many thanks! ...
written 10 months ago by Adam10
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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 10 months ago by Adam10 • updated 10 months ago by Alex Reynolds27k
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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 16 months ago by Adam10 • updated 16 months ago by ATpoint13k
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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 17 months ago by Adam10
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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 17 months ago by Adam10

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