User: Ridha

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Ridha0
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Posts by Ridha

<prev • 9 results • page 1 of 1 • next >
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Analyzing RNA-Seq with duplicate ensembl ids using DESeq2: should tximport be used?
... Greetings!, Hope everyone is doing well! I have a question regarding duplicate ensemble ids of RNA-Seq data. I am using DESeq2 to analyze raw counts from a dataset from the GEO database. I have imported the dataset using read.table and not tximport. From my simple understanding of rna-seq workfl ...
R alignment rna-seq written 14 hours ago by Ridha0
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Comment: C: Analyzing processed RNA-seq data: is this TMM normalized?
... Dear Kevin, Thank you very much for your help, I really appreciate it! I have done what you said and got weird results with only around 250 DEGs. Just to double-check that this is not a problem with the methods I used. I have 3 questions. The dataset(GSE114686) contains 84 samples that are normali ...
written 14 days ago by Ridha0
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Analyzing processed RNA-seq data: is this TMM normalized?
... Greetings! Hope everyone is doing great! I have a question about TMM normalization(pardon me if it seems a simple question as I am still a newbie to this kind of analysis). I want to analyze a publically available RNA-seq dataset(GSE114686). The RNA-seq data is however not raw counts but already pr ...
R rna-seq written 21 days ago by Ridha0 • updated 21 days ago by Kevin Blighe71k
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Annotating gene names: Why having different number of ensembl IDs using biomaRt
... Hello everyone! I have a question regarding the biomaRt package. I have an RNA-seq dataset where gene identifiers are gene names(I think) and I want to retrieve the ensemble id and the description of each gene. However, the results of this annotation is different than the number of the rows I want t ...
gene R rna-seq written 22 days ago by Ridha0 • updated 22 days ago by jared.andrews078.6k
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Comment: C: Design in DESeq2: measruing effects of treatment while adjusting for sample type
... Thank you very much for your reply. I think I got what you mean. However, how would you explain the discrepancies between the PCA plot I produced following ATpoint suggestion and the PCA plot produced from the original paper, knowing that they also used DESeq2 for RNA-seq analysis? I was expecting a ...
written 23 days ago by Ridha0
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Comment: C: Design in DESeq2: measruing effects of treatment while adjusting for sample type
... Thank you very much for your help! I really appreciate it. I did what you said and I got a better PCA plot https://ibb.co/f4zKYDD. However, the RNA-Seq dataset I am using was already used for publication(https://www.sciencedirect.com/science/article/pii/S2211124720308676#bib11) and the PCA plot th ...
written 23 days ago by Ridha0
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Design in DESeq2: measruing effects of treatment while adjusting for sample type
... Hello everyone, I’m doing differential expression analysis using DESeq2 of 6 heart cells(iPSC-CM) that were either treated with iron or not (treatment). The issue is that these 6 samples were taken from 3 different individuals and I am not interested in differences between individuals(sample), but ...
R rna-seq written 24 days ago by Ridha0
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Comment: A: RNA-seq using DESeq2: quality control of replicates using PCA and heatmaps
... Thank you very much for your help! much appreciated! ...
written 5 weeks ago by Ridha0
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RNA-seq using DESeq2: quality control of replicates using PCA and heatmaps
... Hello everyone! I am using DESeq2 for RNA-seq of 6 samples(3 replicates per condition). I have normalized the counts and plotted them using PCA and correlation heatmap to see whether these replicates are similar before proceeding to differential gene analysis. However, I am not sure whether I shoul ...
R rna-seq written 5 weeks ago by Ridha0

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