User: elb

gravatar for elb
elb150
Reputation:
150
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Location:
Torino
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2 days, 23 hours ago
Joined:
6 years, 3 months ago
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Posts by elb

<prev • 51 results • page 1 of 6 • next >
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Comment: C: log transformation of rpkm
... Thank you Kevin! You help me a lot every time! Thank you again! ...
written 22 days ago by elb150
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log transformation of rpkm
... Hi guys, I have a question about how to define a gene to be expressed in RNA Seq analysis. Is it better to use log2(rpkm) or rpkm without log2 transformation to define a gene to be expressed? I know that the log is only a transformation so that log2(rpkm) will let to consider as expressed a gene wit ...
rna-seq written 22 days ago by elb150 • updated 21 days ago by Charles Warden5.6k
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Comment: C: Unsupervised selection of inter-cluster highly variable genes
... Thank you Kevin for your answer. I simply normalized my data and then performed an unsupervised HCA with Pearson correlation as a measure of distance. I have no reference samples. Then the clusters appeared. I appreciate a lot your work. I think I could be inspired by it. Thank you a lot. ...
written 27 days ago by elb150
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Comment: C: Unsupervised selection of inter-cluster highly variable genes
... Oh God. I think I had a problem with the internet connection. Is there a way to remove one of the questions? ...
written 27 days ago by elb150
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(Closed) Unsupervised selection of inter-cluster highly variable genes
... Hi guys, I have a big data.frame of RNA-Seq counts in which rows are genes while columns are samples. I clustered this big matrix and I identified 6 major clusters. They have some common genes, i.e. genes that do not show a huge variation between the samples (around 100 patients) and some genes th ...
variance R rna-seq written 27 days ago by elb150 • updated 27 days ago by genomax58k
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Unsupervised selection of inter-cluster highly variable genes
... Hi guys, I have a big data.frame of RNA-Seq counts in which rows are genes while columns are samples. I clustered this big matrix and I identified 6 major clusters. They have some common genes, i.e. genes that do not show a huge variation between the samples (around 100 patients) and some genes th ...
variance R job rna-seq written 28 days ago by elb150 • updated 27 days ago by Kevin Blighe31k
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Detection p-value Illumina beadchip
... Hi guys, I'm trying to analyse some beadchip data from here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32025. I would like to select genes that are expressed according to the "Detection p-value" criteria. However, this information is not present neither in raw-data nor in the normalized ...
geo illumina beadchip written 4 weeks ago by elb150
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Independent groups normalisation
... Hi guys, I have a question about the normalization of RNA Seq data. I have 3 types of cells of which I would like to identify the differentially expressed genes. As reported in many papers and tutorials, data have to be normalized together. However, I'm afraid that the normalisation could affect t ...
normalization rna-seq written 5 weeks ago by elb150 • updated 5 weeks ago by WouterDeCoster34k
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sva output interpretation
... Hi guys, is there someone who can explain me the meaning of the sva output as from the sva R library? In other words I run svobj = sva(edata,mod,mod0,n.sv=n.sv) as here https://www.bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf but it is not clear to me the meaning of the th ...
sva rna-seq written 6 weeks ago by elb150 • updated 6 weeks ago by Devon Ryan86k
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Comment: C: Illumina bead chip data normalisation
... Thank you very much Kevin! ...
written 7 weeks ago by elb150

Latest awards to elb

Supporter 4 months ago, voted at least 25 times.
Great Question 6 months ago, created a question with more than 5,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 8 months ago, created a question with more than 1,000 views. For regulatory regions discovery and alignment
Popular Question 8 months ago, created a question with more than 1,000 views. For Transcription Factors Annotation
Great Question 3.6 years ago, created a question with more than 5,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Transcription Factors Annotation
Student 3.6 years ago, asked a question with at least 3 up-votes. For Looking For Network Visualization Tools
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Fold Change Detection In Affymetrix Microarray Data Without Replicates
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Looking For Network Visualization Tools
Student 5.9 years ago, asked a question with at least 3 up-votes. For Looking For Network Visualization Tools

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