User: elb
elb • 160
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Posts by elb
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... 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 7 weeks ago by
elb • 160
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... Ciao! Of course! I will edit my question!! ...
written 7 weeks ago by
elb • 160
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... Oh! Sorry! Thank you very much! ...
written 7 weeks ago by
elb • 160
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5 follow
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... 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 ...
written 7 weeks ago by
elb • 160
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... 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 ...
written 7 weeks ago by
elb • 160
• updated
7 weeks ago by
Michael Dondrup ♦ 45k
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Comment:
C: log transformation of rpkm
... Thank you Kevin! You help me a lot every time! Thank you again! ...
written 3 months ago by
elb • 160
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6 follow
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... 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 ...
written 3 months ago by
elb • 160
• updated
3 months ago by
Charles Warden ♦ 5.9k
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221
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... 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 3 months ago by
elb • 160
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... Oh God. I think I had a problem with the internet connection. Is there a way to remove one of the questions? ...
written 3 months ago by
elb • 160
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... 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 ...
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