User: Silvia

Silvia • 10

Reputation:: 10
Status:: New User
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Last seen:: 2 years, 7 months ago
Joined:: 2 years, 7 months ago
Email:: s******************@gmail.com

Posts by Silvia

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Comment: C: FPKM or rlog from DEseq2 for machine learning analysis

... Upps, I thought I replied directly to you! :) Ok, I see the idea. Thank you very much for your help!! Silvia ...

written 2.6 years ago by Silvia • 10

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Comment: A: FPKM or rlog from DEseq2 for machine learning analysis

... thanks Kevin, I obtained the FPKM values with RSEM using the same count matrix that I use to calculate the rlog. Do you have any idea of why these values seem wrong? Also, I have plotted the same values from here https://xenabrowser.net/datapages/?cohort=GTEX using the GTEX data and same value (lo ...

written 2.6 years ago by Silvia • 10

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FPKM or rlog from DEseq2 for machine learning analysis

... I have RNAseq data that I have normalized using RSEM with FPKM and when I make a boxplot per sample to see the normalization plotting the log2(FPKM+0.001), the boxplot is not very good: https://ibb.co/gYgNLm On the other hand, when I plot the normalization using DEseq2 package with rlog, the boxplot ...

normalization fpkm deseq2 rna-seq written 2.6 years ago by Silvia • 10 • updated 15 months ago by Charles Warden ♦ 7.7k

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