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Search: Posts Made By: Michael Love
Forum: Bioinformatics 10-23-2015, 03:43 AM
Replies: 3
Views: 685
Posted By Michael Love
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: 1,924
Posted By Michael Love
Try restarting R. I think if you updated to the...

Try restarting R. I think if you updated to the latest Bioc libs you might need a fresh start to get it working.
Forum: RNA Sequencing 09-30-2015, 04:48 AM
Replies: 1
Views: 907
Posted By Michael Love
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: 2,620
Posted By Michael Love
no, by maximize y over x, I mean that we find the...

no, by maximize y over x, I mean that we find the value of x that gives the largest value of y.

See the figure in the Independent Filtering section of the vignette.

Or we also discuss this in...
Forum: Bioinformatics 09-21-2015, 11:18 AM
Replies: 4
Views: 2,620
Posted By Michael Love
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: 497
Posted By Michael Love
Refer to https://www.biostars.org/p/154250/ for...

Refer to https://www.biostars.org/p/154250/ for answer.
Forum: Bioinformatics 07-28-2015, 06:37 AM
Replies: 1
Views: 576
Posted By Michael Love
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: 1,387
Posted By Michael Love
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: 986
Posted By Michael Love
In DESeq2 we only estimate a single dispersion...

In DESeq2 we only estimate a single dispersion value per gene. See the methods description in the paper:

http://genomebiology.com/2014/15/12/550
Forum: Bioinformatics 07-15-2015, 09:36 AM
Replies: 2
Views: 987
Posted By Michael Love
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: 1,568
Posted By Michael Love
Read the section on the likelihood ratio test in...

Read the section on the likelihood ratio test in the help pages:

?results
Forum: Bioinformatics 07-14-2015, 03:18 AM
Replies: 1
Views: 474
Posted By Michael Love
You can also try featureCounts from the Rsubread...

You can also try featureCounts from the Rsubread package.
Forum: Bioinformatics 07-08-2015, 07:56 AM
Replies: 5
Views: 1,902
Posted By Michael Love
There is a theoretical justification. The sum of...

There is a theoretical justification. The sum of Poisson RVs (random variables) is Poisson. Raw counts of uniquely assigned reads to genes are very close to Poisson distribution across technical...
Forum: Bioinformatics 07-04-2015, 05:40 AM
Replies: 1
Views: 1,614
Posted By Michael Love
For DESeq2, you shouldn't use any kind of values...

For DESeq2, you shouldn't use any kind of values where the library size has been divided out. The statistical methods use the properties of the sampling distribution of counts, as well as estimation...
Forum: Bioinformatics 07-01-2015, 08:09 AM
Replies: 3
Views: 1,132
Posted By Michael Love
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: 39,505
Posted By Michael Love
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: 1,234
Posted By Michael Love
It's not DESeq2, but R's base function 'factor'...

It's not DESeq2, but R's base function 'factor' which determines the order of levels in a factor.

You can control the order of the levels either using the 'contrast' argument, or while you are...
Forum: Bioinformatics 06-26-2015, 04:03 AM
Replies: 3
Views: 1,132
Posted By Michael Love
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: 8,801
Posted By Michael Love
Another test (I suspect there is a column with...

Another test (I suspect there is a column with all zeros):

table(colSums(counts(dds)) == 0)
Forum: Bioinformatics 06-23-2015, 05:25 AM
Replies: 39
Views: 8,801
Posted By Michael Love
what does summary(geoMeans) give you?

what does summary(geoMeans) give you?
Forum: Bioinformatics 06-21-2015, 04:05 AM
Replies: 5
Views: 2,262
Posted By Michael Love
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: 1,361
Posted By Michael Love
"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: 1,072
Posted By Michael Love
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: 39,505
Posted By Michael Love
The first step is the only step which matters how...

The first step is the only step which matters how you generate the counts. This is the step when you build the DESeqDataSet. So you only need to follow the htseq steps up until...
Forum: Bioinformatics 06-09-2015, 11:46 AM
Replies: 2
Views: 1,018
Posted By Michael Love
If you are not familiar with interaction formula...

If you are not familiar with interaction formula in R, I'd recommend splitting into two datasets by treatment and using the '~cow + day' design. This is straightforward to interpret: differences...
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