User: Konstantinos Yeles

Reputation:
20
Status:
New User
Location:
University of Salerno, Salerno, Italy
Scholar ID:
Google Scholar Page
Last seen:
2 hours ago
Joined:
3 years, 11 months ago
Email:
y*****************@gmail.com

PhD student

Posts by Konstantinos Yeles

<prev • 67 results • page 2 of 7 • next >
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Comment: C: Data import with read.delim
... Dear Justin, If you still need to read several txt files at once, I recommend you to read this or this. Furthermore, if you are new to this please  consider reading at least one workflow on how to  perform downstream analysis. RNA-seq workflow: gene-level exploratory analysis and differential expre ...
written 9 months ago by Konstantinos Yeles20
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Comment: C: Normalization for small non-coding RNA and multi-factor design
... design component1.tre component1.unt component2.tre component2.unt total.tre total.unt sample1 1 0 0 0 0 0 sample2 0 1 0 0 0 0 sample3 1 ...
written 9 months ago by Konstantinos Yeles20
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Comment: C: Normalization for small non-coding RNA and multi-factor design
... Dear James, thank you for the answer and your suggestions on this matter. Sorry for the delayed reply. My question is not directly linked to the Scopus of this group, but I have to "gain the necessary expertise by myself". As I couldn't find any publication regarding the issue of  normalization be ...
written 9 months ago by Konstantinos Yeles20
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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 9 months ago by Konstantinos Yeles20 • updated 9 months ago by James W. MacDonald51k
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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 9 months ago by Konstantinos Yeles20
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Comment: C: Normalization for small non-coding RNA
... I will try Biostars! Thank you for your time! ...
written 10 months ago by Konstantinos Yeles20
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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 10 months ago by Konstantinos Yeles20
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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 10 months ago by Konstantinos Yeles20 • updated 10 months ago by António Miguel de Jesus Domingues470
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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 15 months ago by Konstantinos Yeles20
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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 15 months ago by Konstantinos Yeles20

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