User: nazaninhoseinkhan

Reputation:
250
Status:
Trusted
Location:
Iran, Islamic Republic Of
Last seen:
20 hours ago
Joined:
4 years, 8 months ago
Email:
n****************@gmail.com

I am Nazanin Hosseinkhan, PhD in Bioinformatics. My background is Microbiology and I am seeking for a postdoc position.

Posts by nazaninhoseinkhan

<prev • 189 results • page 1 of 19 • next >
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Comment: C: no significant FDR in gene enrichment analysis
... Sure. I will literature searching them. If I understood correctly, the KEGG has not been updated since 2016 and if I do literature searching I might found more pathways than KEGG. Thank you again for your prompt response ...
written 18 days ago by nazaninhoseinkhan250
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Comment: C: no significant FDR in gene enrichment analysis
... Enrichr identified the same pathways as KEGG. I manually searched some of my genes by KEGG. So is it correct if I ignore the FDRs reported by Enrichr? ...
written 18 days ago by nazaninhoseinkhan250
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Comment: C: no significant FDR in gene enrichment analysis
... Hi Kevin, I imported a list of deregulated genes( 30 down vs. 48 up-regulated) resulted from DESEq2 into Enrichr. However, no FDR significant pathways were detected. I checked some of my genes in KEGG and strangely they were detected in the same pathways. I could not understand the meaning of FDR ...
written 18 days ago by nazaninhoseinkhan250
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Comment: C: no significant FDR in gene enrichment analysis
... 52 tumor samples vs 3 normal tissues belong to TCGA project were compared using DESeq2 program. ...
written 21 days ago by nazaninhoseinkhan250
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no significant FDR in gene enrichment analysis
... Dear all, I have a large list of DEGs (around 400). However when I tried to do pathway enrichment analysis using DAVID, PANTHER or Enrichr, based on FDR only 1 pathway was detected. Can u tell me the probable reason for this? Is there anything that I did not consider? Looking forward to your comm ...
fdr enrichment degs rna-seq written 21 days ago by nazaninhoseinkhan250
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Comment: C: removing outliers before running DESeq2
... Thanks a lot for your advice. ...
written 25 days ago by nazaninhoseinkhan250
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Comment: C: removing outliers before running DESeq2
... Thank u so much. Yes, I've already removed genes with lower than 10 reads ...
written 25 days ago by nazaninhoseinkhan250
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removing outliers before running DESeq2
... Dear all, After running DESeq2 program successfully I found out that I had to detect and remove outliers from my htseq count datasets before running DESeq2. However, I am a little confused about how to perform this task. Can u advise me the most straightforward way to do this? Thank u in advance ...
deseq2 outliers rna-seq written 25 days ago by nazaninhoseinkhan250 • updated 25 days ago by arup470
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Comment: C: what logFC or adj-p value cutoff should be chosen when the number of samples in
... As you suggested to me, at first I wanted to normalize all samples together, however, I had to run the analysis on my laptop I run the analysis separately for each race. I will try to repeat the analysis by normalizing all samples together and compare the results. ...
written 4 weeks ago by nazaninhoseinkhan250
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Comment: C: what logFC or adj-p value cutoff should be chosen when the number of samples in
... I am trying to analyze 3 races: Asian(50T, 3N), white(330T,50N) and black\african-american( 28T, 4N). However, I have analyzed not reported groups, but I am not sure if I include them in the analysis. And thank u for the paper. I will read it as soon as possible. ...
written 4 weeks ago by nazaninhoseinkhan250

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