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Forum: Bioinformatics 08-06-2014, 12:53 AM
Replies: 7
Views: 5,779
Posted By velt
The Pearson and Spearman correlation coefficients...

The Pearson and Spearman correlation coefficients are not well suited to RNA-seq count data. Indeed, we want to know if expression values are the same between two samples (linearity => Pearson...
Forum: Bioinformatics 08-05-2014, 07:14 AM
Replies: 3
Views: 1,430
Posted By velt
Thank you for your reply ! This is not a...

Thank you for your reply !
This is not a timeout problem. Indeed, my file weighs only 300 MB.
And even when I split into four equal sized files, and I want to upload these files to UCSC, I have...
Forum: Bioinformatics 08-05-2014, 06:21 AM
Replies: 25
Views: 3,127
Posted By velt
If you want to learn more about DESeq or DESeq2,...

If you want to learn more about DESeq or DESeq2, the documentation is very well done.

DESeq:

http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf

DESeq2:
...
Forum: Bioinformatics 08-05-2014, 05:59 AM
Replies: 25
Views: 3,127
Posted By velt
I advise you to sort your files in ascending...

I advise you to sort your files in ascending order on the "adjusted p-value" column. Thus, the most significant genes are in the beginning of file. Generally a p-value is significant if it is less...
Forum: Bioinformatics 08-05-2014, 05:47 AM
Replies: 3
Views: 1,430
Posted By velt
Problem to display wig files on UCSC.

Hello everyone,

Since the arrival of TopHat2 I completely abandoned the use of TopHat1. The problem is that the "Wiggles" tool of TopHat does not exist for TopHat2. (In addition, the Wiggles tool...
Forum: Bioinformatics 03-05-2014, 02:21 AM
Replies: 1
Views: 1,223
Posted By velt
Plot zero values on x-axis or y-axis with R.

Hello,

I have expression data of several samples generated by RNA-seq (reads count generated by htseq) and I would do a scatterplot of my data in R (two samples by two samples). This is not...
Forum: RNA Sequencing 02-06-2014, 07:59 AM
Replies: 0
Views: 906
Posted By velt
Stranded protocols & study of biotypes

Hello,

I currently use the "TruSeq Stranded Total RNA Sample Prep Kits" of Illumina. I would like to demonstrate the usefulness of this protocol compared to the "standard protocol". So, I wanted...
Forum: Bioinformatics 01-17-2014, 03:09 AM
Replies: 2
Views: 3,454
Posted By velt
Hello, In my view, ​​-inf and inf values,...

Hello,

In my view, ​​-inf and inf values, are effectively due to a division by 0 when calculating the fold-change.

For example in a test_vs_control comparison, inf value for a gene means that...
Forum: Bioinformatics 01-16-2014, 04:42 AM
Replies: 12
Views: 3,099
Posted By velt
Thank you very much for your reply ! I will...

Thank you very much for your reply ! I will proceed in this manner to treat transcripts that overlap.

Have a nice day.
Forum: Bioinformatics 01-16-2014, 02:03 AM
Replies: 12
Views: 3,099
Posted By velt
Dear dpryan, I wrote a script similar to...

Dear dpryan,

I wrote a script similar to your script, to calculate the size of ensembl genes. However, I have a question for you. How you handle transcripts that overlap ?
Indeed, by not taking...
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