User: mimA

gravatar for mimA
mimA30
Reputation:
30
Status:
New User
Location:
European Union
Last seen:
9 months, 2 weeks ago
Joined:
8 years, 10 months ago
Email:
m************@gmail.com

about me

Posts by mimA

<prev • 16 results • page 1 of 2 • next >
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Is FPM the only normalisation method recommended for CircRNAs?
... Hi all, I have a question. For circRNAs detected by RNA-seq, I've read various articles suggesting to use FPM (Fragments per million mapped reads) for normalisation of the raw counts. Is it wrong to use FPKM for circRNA normalisation - the difference being FPKM also corrects for the gene length. T ...
circrna rna-seq normalisation written 9 months ago by mimA30 • updated 9 months ago by Kevin Blighe71k
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Getting GTF for circRNAs
... Hi all, I was wondering how to get a GTF for circRNAs. Does the full GTF from Ensembl (link below) have all coding and non-coding biotypes. ftp://ftp.ensembl.org/pub/current_gtf/homo_sapiens/ Thanks a lot! ...
rna-seq human written 3.4 years ago by mimA30
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Comment: C: Calculating z-scores and p-values from ratios
... ok will do that, thank you! ...
written 4.1 years ago by mimA30
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Comment: C: Calculating z-scores and p-values from ratios
... I have mass spec data which represents proteins in quan values. These values are quite big (in thousands ex. 1000, 1300 2200 and so on). I have been told by our proteomics facility that no further normalisation is required for this data. However, since we wanted expression levels relative to our con ...
written 4.1 years ago by mimA30
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Comment: C: Calculating z-scores and p-values from ratios
... Thanks for your answer Petr. The only thing I'm concerned about is whether its acceptable to use ratios for example like I calculated by dividing with control and use those numbers directly to calculate p-values for example using something like limma?In this way the levels of proteins in each treatm ...
written 4.1 years ago by mimA30
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Comment: C: Calculating z-scores and p-values from ratios
... Thanks for your answer Petr. The only thing I'm concerned about is whether its acceptable to use ratios for example like I calculated by dividing with control and use those numbers directly to calculate p-values for example using something like limma?In this way the levels of proteins in each treatm ...
written 4.1 years ago by mimA30
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Comment: C: Calculating z-scores and p-values from ratios
... Thanks a lot for your reply Shunyip. But I'm just wondering z-score is calculated as (x-mean)/sd. Here x then becomes log2FC values so i end up with 2 z-scores for each protein again ...
written 4.1 years ago by mimA30
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Calculating z-scores and p-values from ratios
... Hello all, I have a question that I can't seem to figure out. I have protein data for 2 different treatments (3 samples each) and only 1 control sample. I want to run some statistics to find differences between the 2 treatment conditions but using the control because it is important for this experi ...
proteomics z-scores p-values statistics written 4.1 years ago by mimA30 • updated 4.1 years ago by Petr Ponomarenko2.7k
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Comment: C: Exon Array Analysis Tools
... Hi Nathan, Just wanted to ask does this do gene-level analysis on exon arrays? Thanks! ...
written 4.2 years ago by mimA30
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Comment: C: p-value and adjusted p-value exactly the same
... ok, will use Limma, thank you!! ...
written 4.2 years ago by mimA30

Latest awards to mimA

Popular Question 2.2 years ago, created a question with more than 1,000 views. For Mapping Chicken Protein Names To Corresponding Gene Names
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Calculating z-scores and p-values from ratios
Popular Question 3.2 years ago, created a question with more than 1,000 views. For p-value and adjusted p-value exactly the same
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Mapping Chicken Protein Names To Corresponding Gene Names

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