User: ezz

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ezz0
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United States
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3 years, 5 months ago
Joined:
3 years, 6 months ago
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e**@winning.com

Posts by ezz

<prev • 5 results • page 1 of 1 • next >
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RNAseq binary transformation
... Why we depend on the raw RNAseq count when we can used binary transformation, 1 for quantile higher 75% over expression and-1 for lower 25% expression? Also, what do you think about clustering to identify subgroups with different survival...then finding the differentially expressed genes, then plot ...
rnaseq tcga binary written 3.4 years ago by ezz0
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Answer: A: Different clustering results of DESeq2 counts and rlog
... Thank you so much...I found out that rlog should not be used in zero infested matrix with large amount of samples. ...
written 3.4 years ago by ezz0
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Different clustering results of DESeq2 counts and rlog
... -After i downloaded the TCGA raw gene counts. I created a DESeq object using Design=~1 -To visualize the normalized effect I ran this code lon <- log2(counts(dds, normalized=TRUE) + 1) -I also ran this code r<-rlog(dds) clustering both matrices results in different outcome.   Any insight? ...
rnaseq deseq2 tcga nomalization written 3.4 years ago by ezz0
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Going crazy with normalizing TCGA raw rsem gene count
... 1-I obtained the RNAseqV2 raw counts, as another post suggested not to use the RSEM.GENE.NORMALIZED as they still contain irregularity as seen on the diag.boxplot 2- I use different methods of normalization to be able to start the clustering analysis. 3-quantile normalization in the preprocess cor ...
rnaseq normalization cancer differential gene expression tcga written 3.5 years ago by ezz0 • updated 7 months ago by Dimitris Vavoulis0
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TCGA RSEM normalized RNAseqV2 counts
... Boxplot of the normalized counts shows different mean and IQR. The expression data is not an affybatch nor eset object to apply rma nor DESeq respectively. Is quantile normalization the way to go?? ...
normalization cancer tcga written 3.5 years ago by ezz0

Latest awards to ezz

Popular Question 3.4 years ago, created a question with more than 1,000 views. For TCGA RSEM normalized RNAseqV2 counts
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Going crazy with normalizing TCGA raw rsem gene count
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Going crazy with normalizing TCGA raw rsem gene count

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