User: elb

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elb160
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Torino
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3 months ago
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Posts by elb

<prev • 56 results • page 1 of 6 • next >
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Comment: C: differential gene expression analysis using log2(counts+1)
... Dear Dott. Blighe, not to complicate my life but I used that package simply because of the group dependent distribution of expression values. Moreover the genes we are interested in, are poorly expressed and so I think the canonical normalisation could flatten the differences because of the mean "sm ...
written 3 months ago by elb160
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Comment: C: differential gene expression analysis using log2(counts+1)
... Ciao! Of course! I will edit my question!! ...
written 3 months ago by elb160
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Comment: C: differential gene expression analysis using log2(counts+1)
... Oh! Sorry! Thank you very much! ...
written 3 months ago by elb160
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differential gene expression analysis using log2(counts+1)
... Hi guys, I know that DESeq as well as EdgeR perform differential gene expression analysis from RNA seq experiments using counts. I have normalized my data.frame using an independent method (qsmooth not in the pipeline of the two packages). The input/output of the normalisation are log2(counts). Now ...
R rna-seq written 3 months ago by elb160
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Align two single cell experiments
... Hi guys, I'm trying to align two single cell experiments using the Seurat package. According to the tutorial here: https://satijalab.org/seurat/Seurat_AlignmentTutorial.html the standard pipeline first performs the FindVariableGenes step and then creates an object from the union of the two datasets ...
R job single cell written 3 months ago by elb160 • updated 3 months ago by Michael Dondrup45k
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Comment: C: log transformation of rpkm
... Thank you Kevin! You help me a lot every time! Thank you again! ...
written 4 months ago by elb160
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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 5 months ago by elb160 • updated 4 months ago by Charles Warden6.4k
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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 5 months ago by elb160
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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 5 months ago by elb160
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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 5 months ago by elb160 • updated 5 months ago by genomax64k

Latest awards to elb

Supporter 8 months ago, voted at least 25 times.
Great Question 10 months ago, created a question with more than 5,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 12 months ago, created a question with more than 1,000 views. For regulatory regions discovery and alignment
Popular Question 12 months ago, created a question with more than 1,000 views. For Transcription Factors Annotation
Great Question 3.9 years ago, created a question with more than 5,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Transcription Factors Annotation
Student 3.9 years ago, asked a question with at least 3 up-votes. For Looking For Network Visualization Tools
Popular Question 6.3 years ago, created a question with more than 1,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 6.3 years ago, created a question with more than 1,000 views. For Fold Change Detection In Affymetrix Microarray Data Without Replicates
Popular Question 6.3 years ago, created a question with more than 1,000 views. For Looking For Network Visualization Tools
Student 6.3 years ago, asked a question with at least 3 up-votes. For Looking For Network Visualization Tools

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