User: asumani

gravatar for asumani
asumani60
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60
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Location:
Istanbul/Turkey
Last seen:
1 week, 5 days ago
Joined:
6 months, 1 week ago
Email:
a******@sabanciuniv.edu

Posts by asumani

<prev • 18 results • page 1 of 2 • next >
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Comment: C: PC1 vs PC2 in separating healthy vs disease
... Many thanks again for this detailed comment! There is no doubt now. ...
written 26 days ago by asumani60
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Comment: C: PC1 vs PC2 in separating healthy vs disease
... Thanks for emphasizing that I shouldn't remove samples. I will check out PC3! ...
written 26 days ago by asumani60
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Comment: C: PC1 vs PC2 in separating healthy vs disease
... I didn't know it was an artifact but I assumed. Your last note makes the plot much more meaningful for me. Could not removing the mixed allergic samples mask the potential differential expression between allergic and control groups? In other words, how can that inter-individual variation can affect ...
written 26 days ago by asumani60
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Comment: C: PCA1 vs PCA2 in separating healthy vs disease
... Yes, I will check those two samples. But my main concern right now is PC2 level clustering. Some of the allergic samples are mixed with control samples on the left bottom part of the plot. How should I interpret it and should I remove allergic samples which are mixed with control samples? ...
written 26 days ago by asumani60
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PC1 vs PC2 in separating healthy vs disease
... Hi all, My samples looks separated on PC2 level. What would it mean if they were clustered on PCA1 level? I think it means lesser variation(since PC2) is accounted between sample groups. I attached my PCA plot. Also, is it logical to remove samples that are mixed(not clearly separated in PC2 leve ...
pca rna-seq written 26 days ago by asumani60
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Comment: C: Gene vs Transcript Level DEG Analysis
... Thanks a lot! I used tximport followed by limma/voom since my other data set was already analyzed with limma. Limma/voom option is also in tximport manual, so I think that is alright. ...
written 4 weeks ago by asumani60
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Gene vs Transcript Level DEG Analysis
... Hi all, I use Ballgown v2.20.0 for DEG analysis after HISAT and StringTie. I conducted both gene and transcript level analysis in ```stattest``` function. In gene level, I got only 50 genes with qval < 0.05. In transcript level, I got 1127 transcripts with qval < 0.05. I want to perform gene ...
ballgown rna-seq written 4 weeks ago by asumani60
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Comment: C: How reproducible is the DEG analysis?
... I believe the number of genes is not similar. They got "substantially expressed" and significant 1412 genes. I got 1170 (FDR < 0.05). However, with abs(logFC) > 0.58 filtering, I got 515 genes at the end. ...
written 6 weeks ago by asumani60
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Comment: C: How reproducible is the DEG analysis?
... > However each difference will cause more differences in the results. I use different tools for each alignment/assembly/DE steps. Maybe that's why I find only common pathways and not the genes. I would like to hear more about this point if possible. >if the study is "on the edge" Also, on y ...
written 6 weeks ago by asumani60
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Comment: C: How reproducible is the DEG analysis?
... Ah, I forgot it. Thanks! I mean 2. ...
written 6 weeks ago by asumani60

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Student 4 weeks ago, asked a question with at least 3 up-votes. For Gene vs Transcript Level DEG Analysis

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