User: Antonio Ahn

gravatar for Antonio Ahn
Antonio Ahn10
Reputation:
10
Status:
New User
Location:
University of Otago
Last seen:
2 months, 1 week ago
Joined:
3 years, 7 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 12 months ago by Antonio Ahn10 • updated 12 months ago by Dario Strbenac1.5k
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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 16 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 16 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 16 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 23 months ago by Antonio Ahn10 • updated 23 months ago by James W. MacDonald52k
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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 3.6 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$symbol ? Sorry i am quite new to R.  ...
written 3.6 years ago by Antonio Ahn10
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DESeq2 plotCount question
... Hi everyone I am trying to do the plotCounts function in DESeq2 and have a question on how to plot for a specific gene that i am interested in.  Wherever i look the codes that is recommended is: plotCounts(dds, gene=which.min(res$padj), intgroup="dex") plotCounts(dds, gene="ENSG____", intgroup= ...
deseq2 written 3.6 years ago by Antonio Ahn10 • updated 3.6 years ago by Michael Love26k

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