User: annamariabugaj

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Posts by annamariabugaj

<prev • 8 results • page 1 of 1 • next >
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Weird results in PANTHER overrepresentation test - Bonferroni count:1 is this possible?
... 0 I encountered a problem while performing analysis using the PANTHER website. I run the statistical overrepresentation test for a genelist of 99 genes (GO-Slim BP, Binomial, Bonferroni) in February 2020. My result was Bonferroni count = 1 and a list of several enriched GO terms. Next we run the s ...
go-slim panther bonferroni go enrichment written 5 months ago by annamariabugaj0
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Comment: C: Removing Batch effect that is the same as condition - DESEq2
... yeah, I know - the problem is I came after the experiments were performed and I am asked to analyse the data... So I am just trying to do it the best way possible. ...
written 7 months ago by annamariabugaj0
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Comment: C: Removing Batch effect that is the same as condition - DESEq2
... Thank you! I have another question - I realised that I can actually split LEARN condition in two different conditions - NEW_room and FAMILIAR-room. In this case could I remove batch effect easier? Llike ~batch+condition? I would have: WT_BASE-batch1 WT_NEW_batch2 WT_FAMILIAR_batch2 I was also ...
written 7 months ago by annamariabugaj0
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Removing Batch effect that is the same as condition - DESEq2
... Hello! Please tell me if my reasoning is correct and how can I do run the proper analysis using DESEq2. I have two batches of RNA-Seq samples: (format: TYPE_condition_batch) WT_BASE_batch1 KO_BASE_batch1 WT_LEARN_batch2 KO_LEARN_batch2 I need to run DGE for WT_BASE and WT_LEARN and I don't ...
deseq2 rna-seq batch effect written 7 months ago by annamariabugaj0 • updated 6 months ago by Biostar ♦♦ 20
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how to create -gct and .cls files from RNASeq counts?
... This is probably a stupid question but I really can not find an answer... I want to compare two DEGs sets from two different experimental settings in order to create a 'common DEGs set' and I found out that GSEA is a good way to do it but I need two types of files .gct and .cls How do I create this ...
.gct deseq2 gsea .cls rna-seq written 12 months ago by annamariabugaj0
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How big are TAD boundaries?
... I have .bed files for TADs from experiments on neuronal fetal tissue downloaded from GEO (GSE77565). I need to extract the boundaries and I am not sure how long they should be. Is it ok to take 5kb flanks as you do for CCD boundaries? ...
neuronal tad written 2.5 years ago by annamariabugaj0 • updated 2.5 years ago by igor12k
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How to compute P_value for Permutation Test?
... I am conducting analyses based on 1000 Genomes paper and I am basically doing the same they did only using my own sets of data. But I am confused if it comes to p value - how do I estimate p value of enrichment(depletion) in such an analyses (the fragment from the 1000 genome paper below describes t ...
permutation genomic intervals p value written 2.7 years ago by annamariabugaj0
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How to download easy "convertable to bed" data form DbVar ?
... Hi, I have a problem with data form DbVar - I need data from autism studies that is easy convertable to .bed since I want to intersect the CNVs with other genomic features. But the .txt file they offer is not tabular - is there any way to get this data in a nice tabular format? Another server maybe ...
sv dbvar data format written 3.5 years ago by annamariabugaj0

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