SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 12 of 12
Search took 0.00 seconds.
Search: Posts Made By: lucer105
Forum: Bioinformatics 12-27-2013, 09:01 PM
Replies: 0
Views: 835
Posted By lucer105
Heatmap question

I used bioconductor gplot draw a heat map with 4 columns with each column has a few thousand genes.

Everything just clumped together, is there anyway to expand the graph?

Thanks
Forum: Bioinformatics 12-13-2013, 07:01 AM
Replies: 3
Views: 2,282
Posted By lucer105
Sounds like it is easy to fix. But I just...

Sounds like it is easy to fix.

But I just wondering, why did my method failed? At least for counting that single gene....
Forum: Bioinformatics 12-12-2013, 10:19 PM
Replies: 3
Views: 2,282
Posted By lucer105
Question Question for making count table for edgeR

I am trying to make a count table for following edgeR..... but after running the edgeR, my marker gene didn't change as it suppose to change. (It suppose to change, confirmed by qPCR, and cuffdiff,...
Forum: Bioinformatics 12-12-2013, 06:55 PM
Replies: 34
Views: 35,185
Posted By lucer105
I think you need a "untreated" control for every...

I think you need a "untreated" control for every time point, or the time will be a extra variable.
Forum: Bioinformatics 12-09-2013, 02:10 PM
Replies: 1
Views: 1,147
Posted By lucer105
Problem solved....................

Problem solved....................
Forum: Bioinformatics 12-09-2013, 01:53 PM
Replies: 1
Views: 1,147
Posted By lucer105
Problems when assembling the transcripts and count reads

I load in bam files, and try to count reads for transcripts for edgeR and DEseq....

### call in the tools
library(GenomicRanges)
library(Rsamtools)
library(DESeq)
library(edgeR)...
Forum: Bioinformatics 12-03-2013, 09:35 PM
Replies: 3
Views: 2,150
Posted By lucer105
Thanks for offering some help. I used galaxy...

Thanks for offering some help.

I used galaxy server at PSU and I do use FTP....same thing.....


"1: a_accepted_hits.bam

An error occurred setting the metadata for this dataset. You may be...
Forum: Bioinformatics 12-02-2013, 08:46 PM
Replies: 3
Views: 2,150
Posted By lucer105
Question about galaxy file uploading (.bam)

I was trying to load my bam files to galaxy (~1.5Gb for each of them).

After they are loaded in Galaxy, it shows the files are all empty, and the file type is .txt, and there is nothing by...
Forum: Bioinformatics 12-01-2013, 07:59 PM
Replies: 6
Views: 2,037
Posted By lucer105
Thanks for the comments. That was exactly the...

Thanks for the comments. That was exactly the purpose----find a few hundred genes well beyond the range of noise. I was thinking by dumping out low read genes and small fold change genes I got more...
Forum: Bioinformatics 12-01-2013, 07:55 PM
Replies: 6
Views: 2,037
Posted By lucer105
Thanks for the comments, what I will do is to...

Thanks for the comments, what I will do is to combine my way with differentally expressed gene programs. The reason that I was asking is to make sure that the first small set of data analysis I did...
Forum: Bioinformatics 12-01-2013, 07:52 PM
Replies: 6
Views: 2,037
Posted By lucer105
Correct me if I am wrong. Do you mean my t-test...

Correct me if I am wrong. Do you mean my t-test actually enrich the false positive read out? As far as I know for edgeR, the inter-replicate variance is within consideration when calculating the...
Forum: Bioinformatics 11-30-2013, 07:13 PM
Replies: 6
Views: 2,037
Posted By lucer105
Am I wrong by doing this?

Hey all~

I am not new to bioinformatics....but I am very new in analyzing RNA-seq data set. I work in a pure wet lab, and I am the only part that is partially dry....

Usually what I do is...
Showing results 1 to 12 of 12

 


All times are GMT -8. The time now is 09:40 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO