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Forum: Illumina/Solexa 07-13-2017, 04:45 AM
Replies: 18
Views: 10,824
Posted By Simon Anders
Not sure whetehr ther's mich point in reviving...

Not sure whetehr ther's mich point in reviving this old thread, hence just to clarify:

Of course, fixed models with empirical Bayes shrinkage cannot replace any form of mixed models. Especially...
Forum: Academic/Non-Profit Jobs 04-29-2017, 07:20 AM
Replies: 0
Views: 418
Posted By Simon Anders
PhD Position for computational scientist in Heidelberg

The new project group of Dr. Simon Anders at the Centre for Molecular Biology of the University of Heidelberg (ZMBH (http://www.zmbh.uni-heidelberg.de)) is researching bioinformatics methodology for...
Forum: RNA Sequencing 07-23-2016, 09:55 AM
Replies: 45
Views: 20,256
Posted By Simon Anders
If each gene is on its own pseudo-contig, you...

If each gene is on its own pseudo-contig, you don't need htseq-count. You just count how often you see each gene ID in the third column of your SAM file which contains the chromosome to which the...
Forum: RNA Sequencing 07-20-2016, 11:57 PM
Replies: 45
Views: 20,256
Posted By Simon Anders
So, each contig/chromosome in your SAM file is a...

So, each contig/chromosome in your SAM file is a gene. This looks like you aligned to a transcriptome but then tried to proceed with a work flow meant for SAM files aligned to a genome.

I think...
Forum: Academic/Non-Profit Jobs 02-10-2016, 03:19 AM
Replies: 0
Views: 464
Posted By Simon Anders
PhD Positions in Helsinki: Molecular Medicine and Bioinformatics

The Institute for Molecular Medicine Finland (FIMM) and the Helsinki Institute for Information Technology (HIIT) invite applications to their PhD programme within the Doctoral Schools of the...
Forum: Bioinformatics 10-29-2015, 06:33 AM
Replies: 191
Views: 60,837
Posted By Simon Anders
Plans, yes -- but I'm so overwhelmed with other...

Plans, yes -- but I'm so overwhelmed with other things that it might take a while till I get to that. Sorry.
Forum: Academic/Non-Profit Jobs 06-30-2015, 03:15 AM
Replies: 0
Views: 755
Posted By Simon Anders
PhD student and post-doctoral position (computational, molecular medicine)

The Institute for Molecular Medicine Finland (FIMM) (http://www.fimm.fi), part of the University of Helsinki and the Nordic EMBL Partnership for Molecular Medicine, is an international research...
Forum: RNA Sequencing 06-21-2015, 07:39 AM
Replies: 45
Views: 20,256
Posted By Simon Anders
Be careful here. In this file, the "exon" lines...

Be careful here. In this file, the "exon" lines only contain transcript IDs ("mRNA_1") but not gene IDs ("gene_1") in their "Parent" fields. This will not work, because if an exon appears in several...
Forum: Bioinformatics 03-10-2015, 01:10 PM
Replies: 6
Views: 1,790
Posted By Simon Anders
Yes, your PCA plot shows that something is amiss,...

Yes, your PCA plot shows that something is amiss, but this has nothing to do with what I discussed above.

You need to figure out what the difference between the sample groups to the left and to...
Forum: Bioinformatics 03-10-2015, 01:04 PM
Replies: 6
Views: 1,790
Posted By Simon Anders
Short answer: Don't worry, it's all fine. The...

Short answer: Don't worry, it's all fine. The values are nearly the same because they should be.

Long answer: Well, this will be long...

This is normal, but a bit unfortunate. In DESeq2, we use...
Forum: Bioinformatics 02-18-2015, 10:46 PM
Replies: 123
Views: 39,892
Posted By Simon Anders
How exactly have you called the "results"...

How exactly have you called the "results" function?

In any case, the first line of the output of the results function indicates the exact comparison that is reported. Can you check whether this...
Forum: Bioinformatics 01-07-2015, 02:52 PM
Replies: 123
Views: 39,892
Posted By Simon Anders
Yes, exactly so.

Yes, exactly so.
Forum: Illumina/Solexa 12-15-2014, 05:27 AM
Replies: 18
Views: 10,824
Posted By Simon Anders
No, because due to the use of an empirical-Bayes...

No, because due to the use of an empirical-Bayes estimation method for dispersion estimation, you do not consume DoFs as usual.

Otherwise, it would be completely impossible to perform comparisons...
Forum: Bioinformatics 11-21-2014, 12:45 AM
Replies: 17
Views: 21,201
Posted By Simon Anders
If you have m samples, then the maximum possible...

If you have m samples, then the maximum possible coefficient of variance is achieved if a gene appears in only one samples and has zero counts in the (m-1) other samples. In these cases, you will see...
Forum: RNA Sequencing 09-26-2014, 11:23 AM
Replies: 11
Views: 2,701
Posted By Simon Anders
That was the point of Alejandro's script: to...

That was the point of Alejandro's script: to replace the apostrophes and semicolons that confused the parser with something else. I have fixed the parser a while ago, however, so there is no need any...
Forum: RNA Sequencing 08-12-2014, 02:57 PM
Replies: 24
Views: 8,772
Posted By Simon Anders
Finally, I have no clue what you mean with p and...

Finally, I have no clue what you mean with p and r. I don't recall using these letters in our paper.
Forum: RNA Sequencing 08-12-2014, 02:56 PM
Replies: 24
Views: 8,772
Posted By Simon Anders
Please don't highjack an old thread to post...

Please don't highjack an old thread to post unrelated questions. This makes it impossible for other readers to find pertinent information.

Also, please don't put several unrealted questions into...
Forum: Bioinformatics 08-12-2014, 05:51 AM
Replies: 191
Views: 60,837
Posted By Simon Anders
I suppose you are right. makes perfect sense. ...

I suppose you are right. makes perfect sense.



I don't think so. I would just need to find the time to do it.

All one needs to do is take all the slots defined for the class in...
Forum: Bioinformatics 08-12-2014, 02:58 AM
Replies: 191
Views: 60,837
Posted By Simon Anders
Yes, the C code is machine generated, but if you...

Yes, the C code is machine generated, but if you look at the pyx files which it is generated from, it should be clearer. Have a look at:
http://www-huber.embl.de/users/anders/HTSeq/doc/contrib.html
Forum: Bioinformatics 08-12-2014, 01:44 AM
Replies: 191
Views: 60,837
Posted By Simon Anders
You asked me this before, but Ididn't reply,...

You asked me this before, but Ididn't reply, right? Sorry about that, I was a bit overwhelmed with mails.

The bad news is: I have no clue why it does not work; I have never worked with the...
Forum: RNA Sequencing 08-06-2014, 05:53 AM
Replies: 35
Views: 20,216
Posted By Simon Anders
To add to Mike's answer: Your FDR of 0.01 is very...

To add to Mike's answer: Your FDR of 0.01 is very stringent. With 0.1 you will get even more genes. But you should not be surprised about that. These seem to be cells cultured in a very...
Forum: RNA Sequencing 07-29-2014, 09:46 PM
Replies: 35
Views: 20,216
Posted By Simon Anders
It is very hard to answer your question without...

It is very hard to answer your question without more information. What is the biology of your experiment? What are you comparing? How do the diagniostic plots (MA plot and dispersion plot) look like?
Forum: RNA Sequencing 07-23-2014, 10:19 PM
Replies: 35
Views: 20,216
Posted By Simon Anders
chocicingwan is right: DESeq1 was too strict with...

chocicingwan is right: DESeq1 was too strict with its dispersion estimates, but the standard way of estimating log fold changes (as also used in DESeq1) partly counters this.

Better use DESeq2's...
Forum: Bioinformatics 06-20-2014, 06:27 AM
Replies: 123
Views: 39,892
Posted By Simon Anders
If you don't show us the MA plot, we can't tell...

If you don't show us the MA plot, we can't tell you whether it looks right. That's why I suggested you post it. Also tell us about the biology of your experiment.

EdgeR's log fold-changes are not...
Forum: Bioinformatics 06-20-2014, 06:06 AM
Replies: 123
Views: 39,892
Posted By Simon Anders
Maybe there is not much happening in your data? ...

Maybe there is not much happening in your data?

Can you post an MA plot?

Also, make sure you understand the conspt of shrunken fold changes. (See our paper...
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