Forum: Bioinformatics
10-23-2015, 03:43 AM
|
|
Replies: 3
Views: 1,472
we discourage users from simultaneously cross...
we discourage users from simultaneously cross posting, because it duplicates the effort of people trying to help
if your post is answered on another forum, you can help out other users and...
|
|
Forum: RNA Sequencing
10-18-2015, 08:49 AM
|
|
Replies: 2
Views: 4,094
|
|
Forum: RNA Sequencing
09-30-2015, 04:48 AM
|
|
Replies: 1
Views: 1,438
One note: this dataset has very low counts...
One note: this dataset has very low counts overall, between 1-10 reads for most genes. Compare with the MA plot for the airway dataset: http://www.bioconductor.org/help/workflows/rnaseqGene/#plots
...
|
|
Forum: Bioinformatics
09-24-2015, 03:27 AM
|
|
Replies: 4
Views: 5,342
|
|
Forum: Bioinformatics
09-21-2015, 11:18 AM
|
|
Replies: 4
Views: 5,342
hi,
The threshold depends on the number of...
hi,
The threshold depends on the number of non-null DE genes which can be recovered by increasing the threshold. The IF procedure comes from the genefilter package with this companion paper:
...
|
|
Forum: Bioinformatics
08-12-2015, 06:45 AM
|
|
Replies: 1
Views: 1,642
|
|
Forum: Bioinformatics
07-28-2015, 06:37 AM
|
|
Replies: 1
Views: 1,728
We discourage simultaneously crossposting...
We discourage simultaneously crossposting identical question on multiple sites.
This duplicates the effort of the answerers (they can't see that a question was answered).
And it also spreads...
|
|
Forum: RNA Sequencing
07-23-2015, 09:46 AM
|
|
Replies: 3
Views: 3,218
This means you want to test the interaction of...
This means you want to test the interaction of treatment and disease, controlling for the individuals within each disease group.
In R formula this is:
~ disease + disease:replicate + treatment...
|
|
Forum: Bioinformatics
07-17-2015, 06:26 AM
|
|
Replies: 2
Views: 3,282
|
|
Forum: Bioinformatics
07-15-2015, 09:36 AM
|
|
Replies: 2
Views: 1,997
Small p-values are expected when you do many...
Small p-values are expected when you do many tests. One way to think about p-value correction is so you are not fooled by these small p-values which are expected under the null. Under the null, you...
|
|
Forum: Bioinformatics
07-14-2015, 03:24 AM
|
|
Replies: 7
Views: 3,015
|
|
Forum: Bioinformatics
07-14-2015, 03:18 AM
|
|
Replies: 1
Views: 1,090
|
|
Forum: Bioinformatics
07-08-2015, 07:56 AM
|
|
Replies: 5
Views: 5,157
|
|
Forum: Bioinformatics
07-04-2015, 05:40 AM
|
|
Replies: 1
Views: 4,033
|
|
Forum: Bioinformatics
07-01-2015, 08:09 AM
|
|
Replies: 3
Views: 2,290
Your code looks correct.
One comment: the...
Your code looks correct.
One comment: the outlier detection is useful when there are a few genes with outliers. Here there are many genes being flagged, which either means: there is a lot of...
|
|
Forum: Bioinformatics
07-01-2015, 07:44 AM
|
|
Replies: 123
Views: 55,754
hi Caitriona
It looks like you have a mix of...
hi Caitriona
It looks like you have a mix of out-of-date and new packages. These often generate conflicts. This can occur if you install Bioconductor packages using install.packages() rather than...
|
|
Forum: Bioinformatics
06-26-2015, 04:09 AM
|
|
Replies: 3
Views: 4,533
|
|
Forum: Bioinformatics
06-26-2015, 04:03 AM
|
|
Replies: 3
Views: 2,290
The best approach would be to combine both...
The best approach would be to combine both analyses into one, by using a DESeqDataSet with all the samples. The design would still be something like: ~ time + condition + condition:time. In order to...
|
|
Forum: Bioinformatics
06-25-2015, 06:19 AM
|
|
Replies: 39
Views: 16,526
|
|
Forum: Bioinformatics
06-23-2015, 05:25 AM
|
|
Replies: 39
Views: 16,526
|
|
Forum: Bioinformatics
06-21-2015, 04:05 AM
|
|
Replies: 5
Views: 5,064
What version of DESeq2 software are you using?...
What version of DESeq2 software are you using? Type: sessionInfo(). The latest release is 1.8, so I'd recommend first checking if updating helps.
Note that DESeq() includes estimateDispersions()...
|
|
Forum: Bioinformatics
06-21-2015, 03:59 AM
|
|
Replies: 11
Views: 2,611
"My question is if the fold change values from...
"My question is if the fold change values from DESeq2 are "wrong"/invalid/whatever, since the counts used to calculate fold change are already normalized (rather than being raw counts, which is what...
|
|
Forum: Bioinformatics
06-17-2015, 12:41 AM
|
|
Replies: 4
Views: 2,350
The order of the rows of the matrix has no...
The order of the rows of the matrix has no difference on the results. You may have a bug in your code?
> dds <- makeExampleDESeqDataSet()
> idx <- sample(1000, 1000, replace=FALSE)
> dds2 <-...
|
|
Forum: Bioinformatics
06-10-2015, 06:39 AM
|
|
Replies: 123
Views: 55,754
|
|
Forum: Bioinformatics
06-09-2015, 11:46 AM
|
|
Replies: 2
Views: 1,881
|
