## User: fkuo

fkuo0
Reputation:
0
Status:
New User
Last seen:
1 year, 10 months ago
Joined:
3 years, 2 months ago
Email:
f******@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

#### Posts by fkuo

<prev • 9 results • page 1 of 1 • next >
1
1.2k
views
1
... Thank you so much! David ...
written 22 months ago by fkuo0
1
1.2k
views
1
... 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 22 months ago by fkuo0
1
1.2k
views
1
... 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 22 months ago by fkuo0
1
1.2k
views
1
... 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 22 months ago by fkuo0
1
1.2k
views
1
... 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 22 months ago by fkuo0
1
1.2k
views
1
... 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 22 months ago by fkuo0
1
1.2k
views
1
... 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, ...
written 22 months ago by fkuo0
0
546
views
0
... [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 3.2 years ago by fkuo0
0
546
views
0
... 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_ ...
written 3.2 years ago by fkuo0

#### Latest awards to fkuo

No awards yet. Soon to come :-)

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.