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Search: Posts Made By: younko
Forum: Bioinformatics 08-31-2014, 11:22 PM
Replies: 10
Views: 2,703
Posted By younko
Oh.. I got it.. It seems that we posted at the...

Oh.. I got it.. It seems that we posted at the same time..
I have updated my posting.. but I got your points!!!!!!!!!

I really appreciate your helps!!!!!!!!!!!!!!!! Thank you SO MUCH!! :)

I...
Forum: Bioinformatics 08-31-2014, 10:21 PM
Replies: 10
Views: 2,703
Posted By younko
Thank you Gordon.. Now, I have a brief...

Thank you Gordon..

Now, I have a brief idea..

Yes. I followed the exact format as EdgeR user guide.


gender patient drug
1 M 1 pre
2 M 1 post
Forum: Bioinformatics 08-31-2014, 09:35 PM
Replies: 10
Views: 2,703
Posted By younko
Unhappy Hm.. This model is the one you suggest.....

Hm..

This model is the one you suggest.. Isn't it?

model.matrix(~gender + gender:drug)
#[1] "(Intercept)" "genderM" "genderF:drugpost" "genderM:drugpost"

In case, I also...
Forum: Bioinformatics 08-29-2014, 12:40 AM
Replies: 10
Views: 2,703
Posted By younko
Smile Thank you Gorden, I tried as you suggest.....

Thank you Gorden,

I tried as you suggest.. but it seems my result looks weird..

when I try my model looks like this

# model.matrix(~drug + drug:gender)
#[1] "(Intercept)" ...
Forum: Bioinformatics 08-29-2014, 12:01 AM
Replies: 10
Views: 2,703
Posted By younko
Thank you so much. However, I still have a...

Thank you so much.

However, I still have a problem. After reading that example, I changed my model like this

model.matrix(~drug + gender + gender:drug)
#[1] "(Intercept)" "drugpost" ...
Forum: Bioinformatics 08-28-2014, 01:28 AM
Replies: 10
Views: 2,703
Posted By younko
One more question: I am trying to do several...

One more question:

I am trying to do several changes..

In the same experimental design,

I created two model..

MODEL1
# model.matrix(~drug + drug:gender)
Forum: Bioinformatics 08-27-2014, 11:37 PM
Replies: 10
Views: 2,703
Posted By younko
EdgeR or GLM model design question

Dear,

I have a question related with my design matrix.
My RNA-seq experimental design looks like this. (paried design)


patient gender drug
sample1 patient1 F Pre
sample2 patinet1 F Post...
Forum: Bioinformatics 08-18-2014, 07:05 PM
Replies: 18
Views: 8,160
Posted By younko
Dear Kopi-o and mikep Thank you for your...

Dear Kopi-o and mikep

Thank you for your comments!!
Here is the specific analysis result I have done!

I have 12 samples from 6 patients with pre- and post- drug treatment.

For my data...
Forum: Bioinformatics 08-17-2014, 11:45 PM
Replies: 18
Views: 8,160
Posted By younko
Dear mikep and mbblack Thank you so much for...

Dear mikep and mbblack

Thank you so much for your comments.
I have one more quick question. I tried to analyze my data to find DEG in two condition. I have used edgeR, DESeq, DESeq2, cuffdiff or...
Forum: Bioinformatics 08-12-2014, 12:36 AM
Replies: 1
Views: 1,027
Posted By younko
DESeq : without replication

Hello

I have a question regarding to the replicates for DESeq.

Here is my data design..

> head(data)

KYM_pre KYM_post GDY_pre GDY_post HKS_pre HKS_post KWK_pre KWK_post PYM_pre PYM_post...
Forum: Bioinformatics 08-07-2014, 06:48 PM
Replies: 18
Views: 8,160
Posted By younko
Thank you for your response.(mikep and mbblack)!!...

Thank you for your response.(mikep and mbblack)!!

Q1 : So, are you recommending the "Wilcoxon signed-rank test " instead of GLM model from edgeR or DESeq?? This would not consider the variation...
Forum: Bioinformatics 08-06-2014, 10:54 PM
Replies: 18
Views: 8,160
Posted By younko
Hello chadn737 I also have similar problems....

Hello chadn737

I also have similar problems.
I do not have a replicate. but I have several patients having same disease.

For example, in my case, I have 10 patients having same disease.
We...
Forum: Bioinformatics 07-16-2014, 06:49 PM
Replies: 6
Views: 1,575
Posted By younko
For the single chromosome plotting, as far...

For the single chromosome plotting,

as far as I know you can use
> plot.cnv.chr(data, chromosome=number, from = xx, to=xx)

I hope it helps,
Forum: Bioinformatics 06-08-2014, 11:28 PM
Replies: 0
Views: 898
Posted By younko
CNV analysis from Exom-seq data

Hello I have a question to analyze the CNV from exome-data using NGS..

I have family (father, mother, affected patient, non-affected sibling)

I would like to find CNV which is associated with...
Forum: Bioinformatics 05-28-2014, 04:34 PM
Replies: 3
Views: 1,224
Posted By younko
oops sorry.. I meant to put it to the title..

When I check the tophat.log file

while it is prining...

[2014-05-28 16:47:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2014-05-28 16:48:02] Mapping...
Forum: Bioinformatics 05-28-2014, 03:59 PM
Replies: 3
Views: 1,224
Posted By younko
Tophat error( sequence and quality are inconsistent)

Hello,

I am trying to map my paried end fastq file to the reference..
I have several samples generated from same library..

However, while I'm mapping the reads to the reference, one of my...
Forum: Bioinformatics 05-18-2014, 05:54 PM
Replies: 2
Views: 1,049
Posted By younko
Please help with cnv-seq output

I read several posting related with cnv-seq output.. but still have some questions. (http://seqanswers.com/forums/showthread.php?t=16882)

When I got the result from cnv-seq, I have th following...
Forum: Bioinformatics 05-15-2014, 04:37 PM
Replies: 6
Views: 1,575
Posted By younko
CNV-seq output (how to know insertion or deletion)

Hello,

I read several postings related with CNV-seq output.
However, I have one more additional question.

The output of CNV-seq looks like this.

cnv chromosome start end ...
Forum: Bioinformatics 05-14-2014, 12:46 AM
Replies: 13
Views: 4,920
Posted By younko
CNV-seq output error

Hello, VanAxel

Sorry for continuous posting.. I am still playing with CNV-seq.
From the cnv file, most of my line's cnv.size, cnv.log2, cnv.p.value havs NA like your posting.. but I have some...
Forum: Bioinformatics 05-14-2014, 12:15 AM
Replies: 13
Views: 4,920
Posted By younko
Nevermind. I found the way.. ...

Nevermind. I found the way..

cnv.print(data,file="xxx") will save the result as you suggest.. though it doesnot show "Gain" column
Forum: Bioinformatics 05-13-2014, 08:07 PM
Replies: 13
Views: 4,920
Posted By younko
Post Hello, VanAxel I have one additional...

Hello, VanAxel

I have one additional question. I got the exact same output file as you show..

chromosome start end test ref position log2 p.value cnv cnv.size cnv.log2 cnv.p.value...
Forum: RNA Sequencing 05-07-2014, 01:25 AM
Replies: 24
Views: 14,629
Posted By younko
good to know

Dear Simon,

I really appreciate your confirmation!
One more quick question.

If I have multiple disease given design. (e.g. paired sample)
how can I handle ?? could you please give some...
Forum: RNA Sequencing 05-06-2014, 06:12 PM
Replies: 24
Views: 14,629
Posted By younko
same for me`

hello sadiexiaoyu

did you get your answers?
I also have exactly same question with you! And I totally agree with your point. As far as I understand your points is right, in that way, we should...
Forum: RNA Sequencing 05-02-2014, 01:06 AM
Replies: 0
Views: 1,110
Posted By younko
Talking DEG analysis with paired sample without replication

I have a question regarding to analyze the RNAseq data.

My data is exactly looks like this.(total 12 samples)

disease1 patient1 pre-hormone
disease1 patient1 post-hormone
disease1 patient2...
Showing results 1 to 24 of 24

 


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