User: fkuo

gravatar for fkuo
fkuo10
Reputation:
10
Status:
New User
Location:
Last seen:
2 years, 1 month ago
Joined:
3 years, 6 months ago
Email:
f******@gmail.com

Posts by fkuo

<prev • 9 results • page 1 of 1 • next >
0
votes
1
answer
1.4k
views
1
answers
Comment: C: [DESeq2] Difference between results from using contrast option and using name op
... Thank you so much! David ...
written 2.2 years ago by fkuo10
1
vote
1
answer
1.4k
views
1
answers
Comment: C: [DESeq2] Difference between results from using contrast option and using name op
... Thanks a lot! By changing the betaPrior to be false a number of thing are changed. First the resultsNames() function result is different. When betaPrior=TRUE (default by DESeq2): [1] "Intercept"    "ResponsePD"   "ResponseSD"   "ResponsePRCR" Now, when betaPrior=FALSE: [1] "Intercept"           ...
written 2.2 years ago by fkuo10
0
votes
1
answer
1.4k
views
1
answers
Comment: C: [DESeq2] Difference between results from using contrast option and using name op
... Hi Michael, Thanks. Sorry for the confusion. I thought I am using DESeq2 and below is my session info. It's DESeq2_1.12.4, right? Even if I set the betaPrior to be true by calling "dds <- DESeq(dds, betaPrior=TRUE)", still got different results between 2 results() calls. Any suggestion for furth ...
written 2.2 years ago by fkuo10
0
votes
1
answer
1.4k
views
1
answers
Comment: C: [DESeq2] Difference between results from using contrast option and using name op
... Hi Michael, Thanks so much. Below is essentially the step for DEG. ################################# dds$Response <- factor(dds$Response,levels=c("PD","SD","PRCR")) # Set the DEG design design(dds) <- ~Response # Run the DEG analysis dds <- DESeq(dds) Response.result1.ihw.PRCRvsPD < ...
written 2.2 years ago by fkuo10
0
votes
1
answer
1.4k
views
1
answers
Comment: A: [DESeq2] Difference between results from using contrast option and using name op
... Hi Michael, Again, thanks for super fast response. Yes, I understand using the 'contrast' argument is the safe way to get the DEG result. But what if someone accidentally used 'name' argument to pull the result and we would like to know the how to interpret the result? Can you please help? Yes, I ...
written 2.2 years ago by fkuo10
0
votes
1
answer
1.4k
views
1
answers
Comment: A: [DESeq2] Difference between results from using contrast option and using name op
... Hi Michael, Thanks for your quick reply. Sorry for the confusion. There are 3 groups of sample in my data set according to response to some treatment. What I want to do is to find the genes up or down regulated in CR/PR group as compared to PD group. Naively I think there are two ways to do it. The ...
written 2.2 years ago by fkuo10
1
vote
1
answer
1.4k
views
1
answer
[DESeq2] Difference between results from using contrast option and using name option of results() function
... Hi there, I have a data set with 3 groups of samples, PD, SD, and CR/PR based on the Response variable. I am interested in finding DEG genes between PD and CR/PR with PD as the reference level. My design is: design(dds)=~Response Normally, in order to get the DEG result, I would call results(dds, ...
deseq2 written 2.2 years ago by fkuo10
0
votes
0
answers
587
views
0
answers
Comment: C: Questions for MEDIPS getPairedGRange function in MEDIPS.readRegionsFile.R
... [Correction] I overlooked the bam file header information. It's bowtie2 not bowtie. Sorry about the confusion. Does anyone know if there's major output differences between bowtie and bowtie2 for paired-end reads? Thanks a lot. ...
written 3.5 years ago by fkuo10
0
votes
0
answers
587
views
0
answers
Questions for MEDIPS getPairedGRange function in MEDIPS.readRegionsFile.R
... Hi there, Below is my biocValid() result. * sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.7 (Final) locale:  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8  [5] LC_MONETARY=en_ ...
medips bam file written 3.5 years ago by fkuo10

Latest awards to fkuo

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 369 users visited in the last hour