User: statfa

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statfa320
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2 years, 5 months ago
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MSc in biostatistics, interested in bioinformatics and statistical genetics

Posts by statfa

<prev • 137 results • page 1 of 14 • next >
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What can be considered as novelty in GWAS?
... Hi, I am asked to conduct a GWAS and to have some novelty in the study too. 1200 cases have a cardiovascular disease and 1800 controls have other types of diseases (such as diabetes, cancers, etc.). Hundereds of thousands of SNPs have been genotyped. What can be considered as novelty when GWAS can ...
gwas snp array snp cardiovascular written 9 days ago by statfa320 • updated 9 days ago by i.sudbery2.4k
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Comment: C: too few differentially expressed genes using each of DESeq2, edgeR and Limma-voo
... Thanks for your reply. The study is about four stages of a disease and I'm gonna conduct differential analysis to find DEGs in these stages using the table of read counts. I have 36, 71, 97 and 67 replicates in each condition and 54000 genes. I filtered out lowly expressed genes and there remaind 2 ...
written 3 months ago by statfa320
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Comment: C: too few differentially expressed genes using each of DESeq2, edgeR and Limma-voo
... Hi, Thanks for your reply In my previous studies, my results seemed ok. In my new study i have 4 conditions (or treatment group) with 36,71,97,67 replicates in each condition. I'm getting strange results. Deseq2 gives no DEGs, edger gives 100 genes and voom gives only 2 genes as differentially exp ...
written 3 months ago by statfa320
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too few differentially expressed genes with large number of replicates, using each of DESeq2, edgeR and Limma-voom
... Hi there. I faced up some strange results when I applied DESeq2, edgeR and Voom on my data. I have worked with these packages on other data and I was always given about more or less than 8000 differentially expressed expressed genes using the FDR<0.05 but this time, DESeq2 gives me no DEG at all ...
degs rna-seq written 3 months ago by statfa320 • updated 3 months ago by Michael Dondrup44k
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Comment: C: How to detect GC content bias and correct them
... Thank you very much genomax. I'll appreciate it. Sorry if I bother a lot. ...
written 6 months ago by statfa320
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Comment: C: How to detect GC content bias and correct them
... And I'm not dumb ;-) I know my posts are available even if I change my username. I changed it because of some other reasons. Don't be so pessimistic. If you look at each of my threads, You will see there are big differences in them ;-) ...
written 6 months ago by statfa320
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Comment: C: How to detect GC content bias and correct them
... Well, actually, @Devon told me to normalize the data by CQN package. But in fact, we should make sure, first, that there is any bias. I wanna know if I'm right about deep tools detecting the GC-content bias. Then, if I find any bias, removing GC-content bias in bam files using deep tools is better o ...
written 6 months ago by statfa320
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Comment: C: How to detect GC content bias and correct them
... It's a different question. There I asked how to find the number of samples in each lane. Nobody knew that. @Devon said if I feel a need to check the bias, then I can do that but he didn't say how. Now I'm asking how. What tools? I searched not only on biostars but on google too. What I learned was t ...
written 6 months ago by statfa320
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How to detect GC content bias and correct them
... Hi guys, I was hoping [here][1] that if one sample is sequenced in each lane, I don't need to correct gc content bias. But now that I don't know how to find number of samples in each lane, I wanna check if GC content bias has occurred. Should I use deep tools (computeGCBias) on galaxy for my rna-s ...
correction gc content detection rna-seq written 6 months ago by statfa320
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Comment: C: Number of samples in each lane in GEO datasets
... Thank you very much. that's my post. Well, I read that in some papers. When only one sample was sequenced in each lane, they didn't bother about GC-content bias. I was hopeful that I could find the information about the number of samples in each lane in GEO datasets so that i didn't need to worry ab ...
written 6 months ago by statfa320

Latest awards to statfa

Autobiographer 9 days ago, has more than 80 characters in the information field of the user's profile.
Popular Question 16 days ago, created a question with more than 1,000 views. For Basic SAMtools tutorial
Popular Question 3 months ago, created a question with more than 1,000 views. For Basic SAMtools tutorial
Popular Question 3 months ago, created a question with more than 1,000 views. For NGS data analysis
Popular Question 3 months ago, created a question with more than 1,000 views. For statistical analysis of WES
Popular Question 6 months ago, created a question with more than 1,000 views. For Basic SAMtools tutorial
Popular Question 6 months ago, created a question with more than 1,000 views. For Basic SAMtools tutorial
Popular Question 7 months ago, created a question with more than 1,000 views. For Basic SAMtools tutorial
Voter 7 months ago, voted more than 100 times.
Centurion 8 months ago, created 100 posts.
Student 14 months ago, asked a question with at least 3 up-votes. For Alignment and mapping
Popular Question 17 months ago, created a question with more than 1,000 views. For Basic SAMtools tutorial
Popular Question 17 months ago, created a question with more than 1,000 views. For Alignment and mapping
Appreciated 19 months ago, created a post with more than 5 votes. For Alignment and mapping
Good Question 19 months ago, asked a question that was upvoted at least 5 times. For Alignment and mapping
Supporter 2.3 years ago, voted at least 25 times.
Student 2.4 years ago, asked a question with at least 3 up-votes. For Alignment and mapping

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