User: yeles.konstantinos

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10
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New User
Location:
University of Salerno, Salerno, Italy
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Google Scholar Page
Last seen:
7 hours ago
Joined:
3 years, 2 months ago
Email:
y*****************@gmail.com

PhD student

Posts by yeles.konstantinos

<prev • 54 results • page 1 of 6 • next >
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Normalization for small non-coding RNA and multi-factor design
... Dear Bioconductor, I would like to ask about the normalization method I should follow regarding the issue of technical variation that a treatment could introduce on top of the extraction of RNA from different components of the cell. Experimental design: > samples group ba ...
normalization limma edger limma voom written 2 days ago by yeles.konstantinos10 • updated 1 day ago by James W. MacDonald48k
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Comment: C: Normalization for small non-coding RNA
... Dear António Miguel de Jesus Domingues, Maybe I misunderstood, but does this mean that a read is counted more than once? Each read should be counted only once. If you want to use multi-mapping reads the best options are to randomly select a piRNA or weight it - read matches two piRNAs, each gets ...
written 15 days ago by yeles.konstantinos10
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Comment: C: Normalization for small non-coding RNA
... I will try Biostars! Thank you for your time! ...
written 16 days ago by yeles.konstantinos10
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Comment: C: Normalization for small non-coding RNA
... Dear Michael Love, Unfortunately, we don't have any artificial (RNA spike-ins?) or endogenous controls. Should I provide more information about the setup?  Sorry for the false information, we have 2 different kinds of spike-ins, one added before treatment and one added after.   ...
written 16 days ago by yeles.konstantinos10
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Normalization for small non-coding RNA
... Dear Bioconductor, Currently, I'm working in piRNA expression in different cell lines and I would like to ask you about the way I can proceed with data transformation and normalization. Now, the main issue is that in order to enrich for piRNAs we performed periodate treatment that "The PO treatment ...
rnaseq smallrna deseq2 tmm written 16 days ago by yeles.konstantinos10 • updated 15 days ago by António Miguel de Jesus Domingues430
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Comment: C: Comparing means of VST tranformed RNA-Seq counts in different groups of samples
... Dear Michael, thank you for your overall suggestions to my questions thus far. Please excuse me to return one last time, but I would like to ask you some quick important questions about the DESeq2 pipeline and the specific functions I have mentioned above, in order to use correctly the normTransfor ...
written 6 months ago by yeles.konstantinos10
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Comment: C: Comparing means of VST tranformed RNA-Seq counts in different groups of samples
... Dear Michael, thank you for your updated answer !! To summarize, in order to confirm your comment and be correct, for the first approach you pinpointed, you mean that i can use  estimateSizeFactorsForMatrix() & normTransform()  for the total dataset, and then subset to the genes of interest, i ...
written 6 months ago by yeles.konstantinos10
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Comment: C: Comparing means of VST tranformed RNA-Seq counts in different groups of samples
... Dear Michael, thank you very much for your answer !! Please excuse me for any misguidance and not provided enough information for my goals-so briefly, these 20 genes, have been identified and selected from another dataset with the same phenotype, based on DE analysis and feature selection. On this ...
written 6 months ago by yeles.konstantinos10
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Comment: C: Comparing means of VST tranformed RNA-Seq counts in different groups of samples
... Hi Benjamin, and thank you for your comprehensive answer and suggestions!! Actually, I have never use the DESeq workflow-only the VST transformation for sample clustering-but I have read the extensive vignette, so my updated comments are:   1)      Because I have only about 20 genes, is it worth t ...
written 6 months ago by yeles.konstantinos10
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Comparing means of VST tranformed RNA-Seq counts in different groups of samples with boxplots
... Dear All, I would like to ask a very specific question about data transformation and the appropriate comparison of groups of samples in gene expression data. In detail, based on raw RNA-Seq data gene counts, I implemented the VST transformation from the DESeq2 R package, for various clustering meth ...
rnaseq deseq2 boxplot vst written 6 months ago by yeles.konstantinos10 • updated 6 months ago by Michael Love20k

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