User: statfa

gravatar for statfa
statfa310
Reputation:
310
Status:
Trusted
Location:
Last seen:
1 month, 3 weeks ago
Joined:
2 years, 3 months ago
Email:
f**************@gmail.com

Posts by statfa

<prev • 136 results • page 1 of 14 • next >
0
votes
1
answer
238
views
1
answers
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 7 weeks ago by statfa310
0
votes
1
answer
238
views
1
answers
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 7 weeks ago by statfa310
7
votes
1
answer
238
views
6 follow
1
answer
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 7 weeks ago by statfa310 • updated 7 weeks ago by Michael Dondrup44k
0
votes
0
answers
316
views
0
answers
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 4 months ago by statfa310
0
votes
0
answers
316
views
0
answers
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 4 months ago by statfa310
0
votes
0
answers
316
views
0
answers
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 4 months ago by statfa310
0
votes
0
answers
316
views
0
answers
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 4 months ago by statfa310
1
vote
0
answers
316
views
0
answers
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 4 months ago by statfa310
0
votes
0
answers
199
views
0
answers
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 4 months ago by statfa310
0
votes
0
answers
199
views
0
answers
Comment: C: Number of samples in each lane in GEO datasets
... Yes, sure. Please read the read count normalization section here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4917940/ ...
written 4 months ago by statfa310

Latest awards to statfa

Popular Question 4 months ago, created a question with more than 1,000 views. For Basic SAMtools tutorial
Popular Question 4 months ago, created a question with more than 1,000 views. For Basic SAMtools tutorial
Popular Question 5 months ago, created a question with more than 1,000 views. For Basic SAMtools tutorial
Voter 6 months ago, voted more than 100 times.
Centurion 6 months ago, created 100 posts.
Student 12 months ago, asked a question with at least 3 up-votes. For Alignment and mapping
Popular Question 15 months ago, created a question with more than 1,000 views. For Basic SAMtools tutorial
Popular Question 15 months ago, created a question with more than 1,000 views. For Alignment and mapping
Appreciated 17 months ago, created a post with more than 5 votes. For Alignment and mapping
Good Question 17 months ago, asked a question that was upvoted at least 5 times. For Alignment and mapping
Supporter 2.2 years ago, voted at least 25 times.
Student 2.3 years ago, asked a question with at least 3 up-votes. For Alignment and mapping

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 949 users visited in the last hour