User: Shucong Li

gravatar for Shucong Li
Shucong Li60
Reputation:
60
Status:
Trusted
Location:
Canada
Last seen:
3 years, 7 months ago
Joined:
5 years, 11 months ago
Email:
l**********@gmail.com

Posts by Shucong Li

<prev • 11 results • page 1 of 2 • next >
0
votes
2
answers
527
views
2
answers
Answer: A: DESeq2 experimental design
... Thanks for your quick reply.  For each animal, there were three sites sampled and tested.  Should I concern about the association among these three sites? ...
written 3.6 years ago by Shucong Li60
0
votes
2
answers
527
views
2
answers
DESeq2 experimental design
... Thanks for help in advance!! My experimental design involves using DESeqs to look at the impact of three diets (diet1, diet2, and diet3) on gene expression at  three sites of animal's gut  (colon, cecum and rectum) .  Each diet was fed to three animals.  All animals were sacrificed at the end of tr ...
deseq written 3.6 years ago by Shucong Li60
0
votes
3
answers
1.2k
views
3
answers
Answer: A: Question: DESeq2 nested design, multifactor test
... Hello Mike, The post I reference is actually this one. https://support.bioconductor.org/p/63134/#63146 Sorry for the mistake and the confusion it caused.  I have revised my original post. Please check it again and help me out. Shucong ...
written 4.5 years ago by Shucong Li60
0
votes
3
answers
1.2k
views
3
answers
Answer: A: Question: DESeq2 nested design, multifactor test
...   Hi Mike, I forgot to mention that the factor "day"  means the calves were sampled on day 36 and day 54. And the data I'm analyzing are NGS 16s RNA illumina data. Basically, we spited calves  into two pens (groups) first. After a couples of weeks of adaption, all calves were samples once (d36) . ...
written 4.5 years ago by Shucong Li60
0
votes
3
answers
1.2k
views
3
answers
Question: DESeq2 nested design, multifactor test
...   Hello Mike, Follow up your post here https://support.bioconductor.org/p/63134/#63146   I'm working on a project with a similar design.   I'm interested to know the effect of "Day" across both groups ('Treatment' and 'Control') of animals.    Thanks in advance. Here are my  experimental de ...
deseq2 experimental design written 4.5 years ago by Shucong Li60
0
votes
1
answer
588
views
1
answers
Answer: A: DESeqs two-factor two-level, interaction is interested
... Hi Michael, I finally got time to try R 3.1.1 with the latest dev version of the packages. The error was not there anymore. Cheers, Shucong Li lishucongnn@gmail.com On Jul 2, 2014, at 11:19 AM, Shucong Li wrote: > Hi Mike, > > I guess you are right. I use R 3.1.0. I notice that R3.1.1 ...
written 5.3 years ago by Shucong Li60
0
votes
1
answer
588
views
1
answer
DESeqs two-factor two-level, interaction is interested
... Hi Mike, I guess you are right. I use R 3.1.0. I notice that R3.1.1 will come out in next a few days. I will then upgrade R and try it again. It the issue still exists, I will let you know. Thanks. Shucong Li lishucongnn@gmail.com On Jun 26, 2014, at 4:45 PM, Michael Love wrote: > hi, > ...
sequencing go phyloseq deseq2 written 5.3 years ago by Shucong Li60
1
vote
1
answer
1.6k
views
1
answer
DESeqs two-factor two-level, interaction is interested
... Hello Michael, I tried to use the latest version of DESeq2 (1.5.20) and phyloseq (1.9.9) to analyze an illumina sequencing data set. However, it didn't work and I got the error: > library(DESeq2) > phyloseq.obj <- seq_all > dds <- phyloseq_to_deseq2(phyloseq.obj,design= ~ Treatme ...
sequencing go phyloseq deseq2 written 5.3 years ago by Shucong Li60 • updated 5.3 years ago by Michael Love25k
0
votes
2
answers
1.3k
views
2
answers
Comment: C: DESeqs two-factor two-level, interaction is interested
... Hi Mike, Thank you. With your help, I finally figured it out, sort of :-) Enjoy the rest of your weekend. Shawn On May 17, 2014, at 11:07 AM, Michael Love wrote: > hi Shawn, > > Let's keep all replies on the Bioconductor mailing list, so other > users can follow the thread. > &g ...
written 5.4 years ago by Shucong Li60
0
votes
4
answers
1.8k
views
4
answers
Comment: C: Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA
... Hi Michael, I have rerun the test with 'blind' set as TRUE. The graph didn't change. It is interesting that rlogTransformation seems to work very well. Please allow me ask one more question about differential analysis with DESeq(). I also run the differential analysis with the same set of dat ...
written 5.9 years ago by Shucong Li60

Latest awards to Shucong Li

Popular Question 3.6 years ago, created a question with more than 1,000 views. For Question: DESeq2 nested design, multifactor test
Popular Question 3.6 years ago, created a question with more than 1,000 views. For DESeqs two-factor two-level, interaction is interested

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 332 users visited in the last hour