User: ugurcabuk

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ugurcabuk20
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New User
Location:
Turkey
Last seen:
6 days, 9 hours ago
Joined:
1 year, 6 months ago
Email:
u**********@gmail.com

Posts by ugurcabuk

<prev • 15 results • page 1 of 2 • next >
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Comment: C: GSVA and SSGSEA for RNA-Seq TPM data
... I Got it. Therefore, I can't apply any thresholds on it. I used ssgsea as method but In the GSVA article, there is no significant difference between gsva and ssgsea, I think. If it really depends on the method I chose, I can change the method but I don't think so the result will change. Z-scores m ...
written 7 days ago by ugurcabuk20
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Comment: C: GSVA and SSGSEA for RNA-Seq TPM data
... Hi Kevin, thank you for reply. I had thougt that like you said about up- and down-regulated in values. However, there were some biases in my result. That's why I am a bit confused. Like, the pathway which belongs to cancer appears up-regulated for all control samples. I did not expect this. After th ...
written 7 days ago by ugurcabuk20
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GSVA and SSGSEA for RNA-Seq TPM data
... Hi, I try to analyze **single sample gene set enrichment analysis** on my data which is RNA-seq gene expression. I'd like to noticed that my data has got continous values not discrete or count. After GSVA, number of the results I got were almost 400 gene sets with enrichment scores. Now, I am a bi ...
R gsva rna-seq written 9 days ago by ugurcabuk20 • updated 7 days ago by Kevin Blighe51k
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Comment: C: Gene Set Enrichment Analysis
... Hi V, I have checked it but unfortunately, I use R script that's why it is not really appropriate for me. Thanks ! ...
written 4 weeks ago by ugurcabuk20
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Comment: C: Gene Set Enrichment Analysis
... Hi Kevin, thank you for answering. Okay I will try to explain my procedure. Firstly, I had rna-seq data then I got fold change value from the data. Now, I will make gene set enrichment analysis. I am a bit confused in this step. What is the difference between getting gene sets from database and crea ...
written 4 weeks ago by ugurcabuk20
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Gene Set Enrichment Analysis
... Hi, I try to apply GSEA on my data. However, I am a bit confused about the process. For example, I have 10000 genes in my gene expression data. As I understood, firstly I should converted the gene names into appropriate gene ID, like gene symbols. Then, I will download gene sets from database, like ...
R gsea rna-seq written 5 weeks ago by ugurcabuk20
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Comment: C: 16s RNA Results
... @Carambakaracho: My goal is to reveal identification of species from sanger sequencing. And yes, it is without OTU clustering. I do not have any pipeline for this purpose. I did make blast from ncbi. After this, Some 23S rRNA sequences of species were given me. I also checked them. But, as i said ab ...
written 6 months ago by ugurcabuk20
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Comment: C: 16s RNA Results
... Sorry for late response. I was very busy after posting. Actually, I do not have any experience about maldi-TOF data because of relating with chemical experiment. Because my role of the experiment is to make bioinformatics analysis. However, maldi-TOF is a result which determines the identification o ...
written 6 months ago by ugurcabuk20
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Comment: C: 16s RNA Results
... Actually, I have sanger sequencing fasta files. I do not have fastq files. Normally, they were ab1 files. But I converted them to fasta files. Basically, they were PCR products, not NGS products. ...
written 7 months ago by ugurcabuk20
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Comment: C: 16s RNA Results
... I will also check it you said. But I dont think so this type of analysis. Because Qiime or Mothur make a cluster analysis, am I right ? ...
written 7 months ago by ugurcabuk20

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