User: Antonio Ahn

gravatar for Antonio Ahn
Antonio Ahn10
Reputation:
10
Status:
New User
Location:
University of Otago
Last seen:
3 months, 1 week ago
Joined:
2 years, 10 months ago
Email:
a*******@gmail.com

Posts by Antonio Ahn

<prev • 8 results • page 1 of 1 • next >
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Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
... Hello, I am finding a significant discrepnacy with RNA-seq expression between TCGA harmonized and legacy datasets for SKCM for a specific gene (SOX10), I have downloaded the TCGA SKCM using the TCGAbiolinks package using the codes below. Following investigation of the SOX10 gene, it is highly expre ...
tcga tcgabiolinks gdc written 4 months ago by Antonio Ahn10 • updated 4 months ago by Dario Strbenac1.4k
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Comment: C: Batch Effect Correction
... Hi Aaron :) Sorry about that confusion. Condition1 and condition2 are the same. I was experimenting with different groupings before and forgot to fix that.  Also, I noticed that the above-mentioned expression changes from removeBatcheffect are occurring in genes that are lowly expressed.      ...
written 7 months ago by Antonio Ahn10
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Comment: C: Batch Effect Correction
... Hi Aaron :) Thank you so much for your response and help. Could I please ask another question? I have noticed that in my top differentially expressed genes (long non-coding RNA genes), that the batch effect adjustment using the removeBatcheffect function (edgeR) significantly alters the expression ...
written 7 months ago by Antonio Ahn10
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Batch Effect Correction
... Hello everyone,  Could I please get an opinion on whether a batch correction is recommended in my data?  Background: I have performed RNAseq gene expression analysis on 2 condition groups. The data was normalised using the rlog function (DEseq2)  (named "Unbatched" in the PCA plot). Subsequently, ...
edger deseq2 batch effect rld removebatcheffect written 7 months ago by Antonio Ahn10
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Unknown gene names in pd.clariom.d.human annotation package
... I have performed a differential gene expression (DEG) analysis using the Clariom D human microrray and pd.clariomd.human (affymetrix-provided) annotation package. In the top 100 DEG list, there are many gene names in lower-case letters that I am unable to identify. This includes names such as "shasm ...
microarray pd.clariom.d.human written 14 months ago by Antonio Ahn10 • updated 14 months ago by James W. MacDonald49k
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Comment: C: DESeq2 plotCount question
... Thank you so much for your help! and also for the recommendation of the short R courses.    ...
written 2.9 years ago by Antonio Ahn10
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Comment: C: DESeq2 plotCount question
... Hi Michael. Would you be able to tell me how i can get the ENSG id for the gene of interest in res$symbol ? Sorry i am quite new to R.  ...
written 2.9 years ago by Antonio Ahn10
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DESeq2 plotCount question
... Hi everyone I am trying to do the plotCounts function in DESeq2 and have a question on how to plot for a specific gene that i am interested in.  Wherever i look the codes that is recommended is: plotCounts(dds, gene=which.min(res$padj), intgroup="dex") plotCounts(dds, gene="ENSG____", intgroup= ...
deseq2 written 2.9 years ago by Antonio Ahn10 • updated 2.9 years ago by Michael Love22k

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