User: CrazyB

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CrazyB210
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6 years, 7 months ago
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Posts by CrazyB

<prev • 54 results • page 1 of 6 • next >
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"high" quality RNA but poor RNAseq results
... Wonder if anyone else on this forum has similar experience with high quality RNA, defined by DV200 metrics, but poor RNAseq results, defined by poor concordance of RNAseq results from different RNAseq platforms. The samples in question are extracted RNA from FFPE samples. As RIN values are generall ...
rna-seq written 5 months ago by CrazyB210 • updated 5 months ago by Charles Warden7.2k
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batch effects of RNAseq data from public databases - need to correct or not ?
... CCLE, TCGA, & GTEx have provided RNAseq data but there was very little information available regarding whether batch effects correction is needed when data from different datasets are combined or compared. I found only one publication that addresses the batch effect, as if batch effects per se i ...
rna-seq written 5 months ago by CrazyB210 • updated 5 months ago by cfos4698130
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Are all RPKM/FPKMs in RNAseq "equal" ?
... I am seeking answers to my specific question and general references for this question - My superficial understanding of RPKM is the term is a unit of RNA-seq output and refers to read per kilobase per million read. The calculation takes into account the library size and mRNA length to provide a gen ...
rpkm rna-seq written 5 months ago by CrazyB210 • updated 5 months ago by Charles Warden7.2k
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Comment: C: anyone with experience of RNAseq from FFPE samples on Novaseq vs. that on Hiseq
... @genomax. Thanks for sharing. I will seek input at seqanswers regarding prep kits. ...
written 7 months ago by CrazyB210
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anyone with experience of RNAseq from FFPE samples on Novaseq vs. that on Hiseq
... I was wondering if anyone on this forum has hands-on experience with RNAseq from FFPE samples running on Novaseq vs. Hiseq machines. From the whitepaper, it's clear Novaseq has a bigger capacity to handle more reads. What's not clear to me is how good the performance is for the new library prep kit ...
novaseq rna-seq hiseq written 7 months ago by CrazyB210 • updated 7 months ago by genomax71k
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Comment: C: references for fold-change cutoff
... Our decision tree is as follows - 1. calculate the fold-change with FDR 2. remove all genes that have FDR >=0.05 3. rank the remaining genes based on fold-changes 4. make an arbitrary cutoff of the fold-change - we set it at a low end (1.2-fold) 5. pool all genes that fulfill the FDR and fold-ch ...
written 10 months ago by CrazyB210
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Answer: A: references for fold-change cutoff
... [cancelled by OP - should be a comment not an answer] ...
written 10 months ago by CrazyB210
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references for fold-change cutoff
... To my knowledge, there is no consensus cutoff value for the fold-change in transcriptomic data (correct me if this is wrong). However, one reviewer for a submitted manuscript asked that we provide references to support our cutoffs for significance selected. I wonder if there are "good" references ...
cutoff transcriptome fold-change written 10 months ago by CrazyB210 • updated 10 months ago by Fabio Marroni2.3k
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median probe intensity does not correlate with RNA-seq data - what's the best practice to compare the expression data?
... Looking at RNA-seq data from CCLE (Cancer Cell Line Encyclopedia) from Broad Institute and microarray expression data from NCI-60 cell lines, there is a discrepancy in the "relative" expression level of genes of my interest. Thus I was wondering if there is a "best practice" when we try to pull data ...
microarray rna-seq written 11 months ago by CrazyB210
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Comment: C: looking for large human genomes databases
... @ lltommy, @ genomax, my title said that i am looking for human genomes databases. I've now made the changes in the main text to reflect that. ...
written 2.1 years ago by CrazyB210

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Popular Question 7 months ago, created a question with more than 1,000 views. For a question about some "basic numbers" for rna-seq experiments
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Popular Question 24 months ago, created a question with more than 1,000 views. For how to add pedigree info into VCF
Popular Question 24 months ago, created a question with more than 1,000 views. For is there a value of ranking genes based on p-value in RNA-seq data
Popular Question 24 months ago, created a question with more than 1,000 views. For a question about some "basic numbers" for rna-seq experiments
Good Question 3.0 years ago, asked a question that was upvoted at least 5 times. For What Is Considered A Good Coverage Depth In Exon Capture Seq
Popular Question 3.0 years ago, created a question with more than 1,000 views. For a question about some "basic numbers" for rna-seq experiments
Popular Question 3.0 years ago, created a question with more than 1,000 views. For how to find SNP positions (for non-bioinformaticians)
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Multiplex In Exome Seq And "Customized/Capture" Seq Kits
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Epic Question 3.5 years ago, created a question with more than 10,000 views. For convert text file to VCF file ?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For convert text file to VCF file ?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Multiplex In Exome Seq And "Customized/Capture" Seq Kits
Popular Question 3.5 years ago, created a question with more than 1,000 views. For What Is Considered A Good Coverage Depth In Exon Capture Seq
Great Question 4.0 years ago, created a question with more than 5,000 views. For convert text file to VCF file ?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Multiplex In Exome Seq And "Customized/Capture" Seq Kits
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Negative B-Statistic Values In Limma/Microarray Differential Expression

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