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Forum: Illumina/Solexa 02-19-2019, 04:51 AM
Replies: 4
Views: 1,484
Posted By David [R]
Thanks a lot.

Thanks a lot.
Forum: Illumina/Solexa 02-19-2019, 02:42 AM
Replies: 4
Views: 1,484
Posted By David [R]
Thanks a lot for your reply Jafar, As far as...

Thanks a lot for your reply Jafar,

As far as pooling goes, apparently it gave good results in the MiSeq. As for primer dimers, correct me if I a wrong, if this was the case those reads would have...
Forum: Illumina/Solexa 02-19-2019, 12:08 AM
Replies: 4
Views: 1,484
Posted By David [R]
NovaSeq uneven lib sizes: any tagwise bias?

Hi,
I just got my first NovaSeq-produced RNASeq dataset and the obtained lib sizes are quite uneven. The attached file shows the lib sizes. If you look at it, you’ll see that there are three libs...
Forum: RNA Sequencing 07-23-2015, 04:29 AM
Replies: 4
Views: 3,028
Posted By David [R]
Thanks a lot!

Thanks a lot!
Forum: RNA Sequencing 07-23-2015, 04:11 AM
Replies: 4
Views: 3,028
Posted By David [R]
Hi dpryan, THanks for your reply. Yes, that...

Hi dpryan,

THanks for your reply. Yes, that is right. My only only doubt came from de fact that if normalized.lib.sizes=TRUE, then the cpm are calculated using the normalization factors, which I...
Forum: RNA Sequencing 07-23-2015, 01:04 AM
Replies: 4
Views: 3,028
Posted By David [R]
edgeR, "DGELIst" function, "group" parameter

Hi,

I am using edgeR for some RNASeq analysis. My question concerns the DGEList function and its "group" parameter. I realized that, whether doing group=mydesignfactor or...
Forum: RNA Sequencing 07-24-2012, 01:07 AM
Replies: 3
Views: 1,865
Posted By David [R]
NA and not NaN

Hi,

Just to correct the previous post: it is NA that I get on my fits, and not NaN.
On the other hand, everytime I get them, they concern the "symptoms" factor. However, I do not get them...
Forum: RNA Sequencing 07-23-2012, 07:51 AM
Replies: 3
Views: 1,865
Posted By David [R]
code

Hi Simon,

Thanks for your post.
Please find here below the links towards the code and the RData itself.
I guess the problem comes from working on multi-factorial with no replicates, but I am...
Forum: RNA Sequencing 07-20-2012, 06:39 AM
Replies: 2
Views: 2,165
Posted By David [R]
Thanks a lot!

Thanks a lot!
Forum: RNA Sequencing 07-20-2012, 05:37 AM
Replies: 2
Views: 2,165
Posted By David [R]
CG content and Illumina Sequencing

Hi,

We are having some problems sequencing DNA regions with a GC% higher than 75 in a bacteria with a GC average content of 67%. We are not completely sure whether the problem comes from the...
Forum: RNA Sequencing 07-19-2012, 11:17 PM
Replies: 3
Views: 1,865
Posted By David [R]
NaN on fitNbinomGLMs using DESeq

Hi,

I am doing some RNASeq analysis and, for some of the fitNbinomGLMs I get NaN scores on some of the factors
Any idea on why this would be and how to sort it out?
For info the design is kind...
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