User: stan

gravatar for stan
stan70
Reputation:
70
Status:
Trusted
Location:
Pretoria, South Africa
Last seen:
1 week, 1 day ago
Joined:
4 years, 11 months ago
Email:
s*********@gmail.com

Posts by stan

<prev • 16 results • page 1 of 2 • next >
0
votes
0
answers
2.5k
views
0
answers
Comment: C: n.sv number for batch effects in RNA-seq
... Hi vcrhis_ngs, In your comment above, which package is the "plPCA" function from, I can't seem to find it anywhere. Or if it was a typo, what's the actual function/package name you used to draw your corrected PCA? Thanks, ...
written 6 months ago by stan70
0
votes
2
answers
9.3k
views
2
answers
Comment: C: Deseq2: Time series experiment with 2 conditions and 5 time points
... Hi Deni, i doubt doing so will give you pairwise comparisons between the two conditions? perhaps i am missing something in your statement. The answers provided in the link above worked fine for me. Cheers Stan ...
written 2.1 years ago by stan70
0
votes
0
answers
1.8k
views
0
answers
Comment: C: Strange MA-plot using DESeq2
... [Here][1] is the scatter plot of the raw counts between one VC and LTNP samples. [1]: https://s17.postimg.org/7fnrztkfj/Scatter_Plot_VCvs_LTNP_1.png ...
written 2.3 years ago by stan70
0
votes
0
answers
1.8k
views
0
answers
Comment: C: Strange MA-plot using DESeq2
... > sizeFactors(dds) EC_1.count EC_2.count EC_3.count LTNP_1.count 4.69209178 4.68776603 4.46989074 5.10407662 LTNP_2.count LTNP_3.count LTNP_4.count VC_1.count 4.88086201 3.97763836 6.47169000 0.07196773 VC_2.count V ...
written 2.3 years ago by stan70 • updated 2.3 years ago by WouterDeCoster37k
0
votes
0
answers
1.8k
views
0
answers
Comment: C: Strange MA-plot using DESeq2
... I used raw counts generated using HTSeq. I think my design is OK, it's as follows: ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design=~condition) I only have one variable "condition", which has three levels (EC, VC, LTNP). ...
written 2.3 years ago by stan70
0
votes
0
answers
1.8k
views
0
answers
Comment: C: Strange MA-plot using DESeq2
... I just followed the steps as outlined in the DESeq2 manual. Could there be a problem with my group "VC" samples? which is causing the 99% variance? ...
written 2.3 years ago by stan70
0
votes
0
answers
1.8k
views
0
answers
Comment: C: Strange MA-plot using DESeq2
... I have added the analysis steps. These are samples from HIV-positive individuals grouped according to viral load ...
written 2.3 years ago by stan70
7
votes
0
answers
1.8k
views
8 follow
0
answers
Strange MA-plot using DESeq2
... Hello, I am using DESeq2 to perform some differential expression analysis between 3 levels of a disease condition. However, I am getting a strange looking MA-plot when i compare some of the conditions. I am trying to understand what could be the reason for the skewness in my MA-plot. Any help will ...
R deseq2 rna-seq written 2.3 years ago by stan70 • updated 2.2 years ago by Biostar ♦♦ 20
3
votes
2
answers
9.3k
views
2
answers
Answer: A: Deseq2: Time series experiment with 2 conditions and 5 time points
... So, I found the answer for my question in one of the Deseq2 threads at the bioconductor support forum, a nice explanation is given and the thread is found here: https://support.bioconductor.org/p/65676/#66860 incase it might be of use to someone else. ...
written 3.9 years ago by stan70
4
votes
2
answers
9.3k
views
2
answers
Deseq2: Time series experiment with 2 conditions and 5 time points
... Hi all, I have done a time series analysis using the steps outlined below and I got differentially expressed genes showing a condition-specific effect (according to the example at http://www.bioconductor.org/help/workflows/rnaseqGene/#time) > sampleTable<-data.frame(sampleName=sampleFiles, ...
R deseq2 rna-seq written 3.9 years ago by stan70 • updated 2.1 years ago by deni.ribicic0

Latest awards to stan

Popular Question 12 months ago, created a question with more than 1,000 views. For Deseq2 error using HTSeq input for 10 samples with 3 replicates each
Great Question 2.0 years ago, created a question with more than 5,000 views. For Deseq2: Time series experiment with 2 conditions and 5 time points
Supporter 2.1 years ago, voted at least 25 times.
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Deseq2 error using HTSeq input for 10 samples with 3 replicates each
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Deseq2: Time series experiment with 2 conditions and 5 time points
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Deseq2: Time series experiment with 2 conditions and 5 time points
Scholar 3.9 years ago, created an answer that has been accepted. For A: Deseq2: Time series experiment with 2 conditions and 5 time points

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1692 users visited in the last hour