Forum: Sample Prep / Library Generation
11-17-2014, 11:11 PM
|
|
Replies: 5
Views: 1,581
Transcriptome sequencing for differential...
Transcriptome sequencing for differential expression is basically high throughput qPCR. You can't get qPCR published without biological replicates, if you tried to published qPCR with a single pool...
|
|
Forum: Bioinformatics
09-15-2014, 02:54 AM
|
|
Replies: 1
Views: 2,265
Your problem is probably from this line
...
Your problem is probably from this line
geneList <- factor(as.integer(geneNames %in% myInterestingGenes))
geneNames %in% myInterestingGenes will return a vector of TRUE / FALSE of length...
|
|
Forum: RNA Sequencing
08-28-2014, 08:53 PM
|
|
Replies: 15
Views: 23,483
|
|
Forum: RNA Sequencing
08-28-2014, 08:28 PM
|
|
Replies: 15
Views: 23,483
|
|
Forum: Bioinformatics
08-05-2014, 08:26 PM
|
|
Replies: 34
Views: 14,532
|
|
Forum: Bioinformatics
07-31-2014, 06:29 PM
|
|
Replies: 2
Views: 2,799
|
|
Forum: Bioinformatics
07-24-2014, 02:04 AM
|
|
Replies: 3
Views: 1,952
|
|
Forum: Bioinformatics
07-23-2014, 02:49 AM
|
|
Replies: 2
Views: 2,987
|
|
Forum: Bioinformatics
07-18-2014, 02:19 AM
|
|
Replies: 24
Views: 15,540
|
|
Forum: Bioinformatics
07-18-2014, 01:28 AM
|
|
Replies: 24
Views: 15,540
|
|
Forum: Bioinformatics
07-18-2014, 12:38 AM
|
|
Replies: 24
Views: 15,540
|
|
Forum: Bioinformatics
07-17-2014, 07:56 PM
|
|
Replies: 24
Views: 15,540
You need to use a transcriptome assembler...
You need to use a transcriptome assembler (SOAPdenovo-Trans, Trinity, Trans-abyss etc.), of course a genome assembler will fail with RNA-seq data, almost all of the assumptions regarding the data are...
|
|
Forum: Bioinformatics
07-15-2014, 07:38 PM
|
|
Replies: 43
Views: 27,446
Those are two different tests, but you are...
Those are two different tests, but you are overwriting the first reslt object (res) with the second.
res <- nbinomTest( cds, "A-mock", "A-infect", )
res <- nbinomTest( cds, "B-mock", "B-infect",...
|
|
Forum: The Pipeline
07-14-2014, 08:51 PM
|
|
Replies: 52
Views: 204,601
|
|
Forum: Bioinformatics
07-01-2014, 01:23 AM
|
|
Replies: 1
Views: 1,731
|
|
Forum: Bioinformatics
05-27-2014, 09:11 PM
|
|
Replies: 2
Views: 1,146
call that string MyString
NewString <-...
call that string MyString
NewString <- paste("mygenes_", MyString, sep="")
If that is a column of a data frame called DF
DF$MyString <- paste("mygenes_", DF$MyString, sep="")
|
|
Forum: Bioinformatics
05-21-2014, 02:41 AM
|
|
Replies: 4
Views: 2,871
I think R needs to be compiled with tcl/tk...
I think R needs to be compiled with tcl/tk already installed. Some packages need the dev version of tcl/tk and won't work with the normal version.
What does R say when you give it:...
|
|
Forum: Illumina/Solexa
05-15-2014, 10:59 PM
|
|
Replies: 8
Views: 7,621
The TruSeq DNA PCR-Free kit claims to have...
The TruSeq DNA PCR-Free kit claims to have "Superior genomic coverage with radically reduced library bias and gaps" compared to the original TruSeq DNA kits. I have been recommended to do multiple...
|
|
Forum: Bioinformatics
05-08-2014, 02:14 AM
|
|
Replies: 2
Views: 1,620
It might be more effective to exclude...
It might be more effective to exclude mitochondrial sequence after the assembly, the mitochondria and chloroplast tend to form separate contigs anyway. Unless your plant species is Arabidopsis, only...
|
|
Forum: Bioinformatics
05-08-2014, 01:55 AM
|
|
Replies: 24
Views: 15,540
|
|
Forum: Ion Torrent
04-17-2014, 12:33 AM
|
|
Replies: 2
Views: 2,413
|
|
Forum: Bioinformatics
04-02-2014, 08:40 PM
|
|
Replies: 6
Views: 2,078
|
|
Forum: Bioinformatics
04-02-2014, 08:31 PM
|
|
Replies: 6
Views: 1,597
lets assume that table with the annotation is...
lets assume that table with the annotation is called "annot" and it has the comumn with the An01g00010 entries also called "ID" the you want:
New <- merge(res.combined,annot,by="ID",all.x=T,sort=F)...
|
|
Forum: RNA Sequencing
03-28-2014, 12:27 AM
|
|
Replies: 6
Views: 4,909
The object res has the results for all of the...
The object res has the results for all of the genes and their FDR adjusted p-values. I always just merge res with the corrected count data and then write it all out to a tab delimited table then you...
|
|
Forum: RNA Sequencing
03-26-2014, 08:38 PM
|
|
Replies: 6
Views: 4,909
|
