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Forum: Bioinformatics 05-20-2013, 09:34 AM
Replies: 1
Views: 1,041
Posted By rfilbert
Aligning Chimeric Reads

Hi there,

Which aligners can handle chimeric reads? I see several threads about this but I can't find an answer.

Thanks!
Robert
Forum: Bioinformatics 01-19-2013, 08:31 AM
Replies: 69
Views: 12,182
Posted By rfilbert
I can't see any harm in effective variance...

I can't see any harm in effective variance stabilization, and big benefits to it.
Forum: Bioinformatics 01-19-2013, 06:12 AM
Replies: 9
Views: 9,547
Posted By rfilbert
Do you want to remove all sequences with N's or...

Do you want to remove all sequences with N's or just remove the N's from the file? I agree with kmcarr that they are there for a very important reason. I'm not a vi guru, but I don't think that...
Forum: Bioinformatics 01-19-2013, 06:02 AM
Replies: 69
Views: 12,182
Posted By rfilbert
My big problem with these overly simplistic...

My big problem with these overly simplistic filtering approaches can be illustrated with your 3rd experiment design, where you have 3 categories: Control, Treatment A, and Treatment B. Assuming a...
Forum: RNA Sequencing 01-17-2013, 03:38 AM
Replies: 25
Views: 9,007
Posted By rfilbert
Calling your argument an elephant in the room is...

Calling your argument an elephant in the room is just your way of insulting me. As I've already stated, I understand that by reducing the gene list, FDR becomes less stringent. You really don't need...
Forum: RNA Sequencing 01-17-2013, 12:22 AM
Replies: 25
Views: 9,007
Posted By rfilbert
Partek is not a black box, and I am unaware of...

Partek is not a black box, and I am unaware of any proprietary algorithms in their software. When we were first considering different software packages for our microarray analysis, our statistician...
Forum: RNA Sequencing 01-16-2013, 11:51 PM
Replies: 25
Views: 9,007
Posted By rfilbert
First of all, I don't think it is wise or...

First of all, I don't think it is wise or friendly of you to assume that if I don't agree with your approach, I have not read the literature or are somehow less learned than you are. I will ignore...
Forum: RNA Sequencing 01-16-2013, 08:49 PM
Replies: 25
Views: 9,007
Posted By rfilbert
I understood all that the first time you...

I understood all that the first time you explained it. However, you've just pulled the numbers 5 and 20 out of thin air - not from real data or even simulated data. Why not do something useful and...
Forum: RNA Sequencing 01-16-2013, 06:57 PM
Replies: 25
Views: 9,007
Posted By rfilbert
What black box am I putting my data into? BTW, I...

What black box am I putting my data into? BTW, I fully understand how FDR works and why a smaller starting list results in a less stringent FDR. Apparently, however, you have missed my point. Since...
Forum: RNA Sequencing 01-16-2013, 05:06 PM
Replies: 25
Views: 9,007
Posted By rfilbert
Um, if you filter out a gene that is truly...

Um, if you filter out a gene that is truly differentially expressed, that is a false negative. Are you a statistician? Seems you are not.
Forum: RNA Sequencing 01-16-2013, 06:29 AM
Replies: 25
Views: 9,007
Posted By rfilbert
Clearly you have little background or access to a...

Clearly you have little background or access to a real statistician. Hello World! You must filter out low abundance transcripts - they are clearly not important!
Forum: RNA Sequencing 01-16-2013, 06:26 AM
Replies: 25
Views: 9,007
Posted By rfilbert
why pre-filter at all? It is only an opportunity...

why pre-filter at all? It is only an opportunity for false negatives. I think the only reason for filtering is software that can't handle the whole genome.
Forum: RNA Sequencing 01-16-2013, 06:10 AM
Replies: 25
Views: 9,007
Posted By rfilbert
pre-filtering is a bad idea. Why do people do it?...

pre-filtering is a bad idea. Why do people do it? Because the software can't handle large data?
Forum: Bioinformatics 01-16-2013, 06:07 AM
Replies: 37
Views: 8,023
Posted By rfilbert
It was inevitable that the commercial software...

It was inevitable that the commercial software vendors would recommend their own tools on this thread. If I want to go commercial, why do I want to pay Integromics and also pay Spotfire for this?...
Forum: Bioinformatics 01-13-2013, 10:44 PM
Replies: 37
Views: 8,023
Posted By rfilbert
Not quite getting the tupperware analogy, but I...

Not quite getting the tupperware analogy, but I take it from your logic that Ford charges 300% of a fair price for a car, and the solution is for the government to create a new tax to make cars and...
Forum: Bioinformatics 01-13-2013, 05:52 PM
Replies: 37
Views: 8,023
Posted By rfilbert
I would like to add my persspective on "freeware"...

I would like to add my persspective on "freeware" - it's absolutely not free! Besides the cost of hiring bioinformaticians to stitch it all together, it is paid for by the taxpayers - usually in the...
Forum: Bioinformatics 01-07-2013, 10:43 PM
Replies: 40
Views: 13,516
Posted By rfilbert
Well if you want to debate this with the...

Well if you want to debate this with the statisticians at Partek, feel free. I use it and like as do many of my colleagues. As you said, you are not a statistician either, and I don't know about...
Forum: Bioinformatics 01-07-2013, 10:16 PM
Replies: 40
Views: 13,516
Posted By rfilbert
In my case, some of the genes were differentially...

In my case, some of the genes were differentially expressed between tumor and normal, while others were not, but some of them were differentially expressed between ER+ and ER-. As a fellow biologist,...
Forum: Bioinformatics 01-07-2013, 05:55 PM
Replies: 40
Views: 13,516
Posted By rfilbert
Well, you could estimate variance if you really...

Well, you could estimate variance if you really wanted, and could rank genes by p-value and/or fold change. One way you could do that is to assume a Poisson distribution, where the variance is equal...
Forum: Bioinformatics 01-07-2013, 04:49 PM
Replies: 40
Views: 13,516
Posted By rfilbert
I guess you are saying that as a researcher, I...

I guess you are saying that as a researcher, I can only have 1 hypothesis, and only about 1 factor, and it must be the same for every gene. That is not how a biologist thinks. We want to learn what...
Forum: Bioinformatics 01-07-2013, 04:45 PM
Replies: 40
Views: 13,516
Posted By rfilbert
Really? Are you sure? In my case, the samples are...

Really? Are you sure? In my case, the samples are from a breast cancer study. Some of the samples are tumor and some are normal. Some are ER+ and some are ER-. Partek Flow tested each gene to see...
Forum: Bioinformatics 12-26-2012, 08:25 AM
Replies: 40
Views: 13,516
Posted By rfilbert
Actually, it only does call more...

Actually, it only does call more genes/transcripts because of better fit, not because of multiple testing. The reason is that Partek Flow is not picking the model with the best p-value, it is picking...
Forum: Bioinformatics 12-21-2012, 11:36 AM
Replies: 40
Views: 13,516
Posted By rfilbert
There are multiple options for normalization, but...

There are multiple options for normalization, but I believe the default option is to simply normalize to the total number of reads for each sample. I don't think any normalization based on the length...
Forum: Bioinformatics 12-21-2012, 11:04 AM
Replies: 40
Views: 13,516
Posted By rfilbert
I would definitely recommend Partek Flow for the...

I would definitely recommend Partek Flow for the following reasons:
1. They fit 5 different distribution assumptions and use the best fit for each gene or transcript. This gives more statistical...
Forum: Bioinformatics 12-21-2012, 10:22 AM
Replies: 40
Views: 13,516
Posted By rfilbert
I'm not sure what SAS's JMP Genomics team is up...

I'm not sure what SAS's JMP Genomics team is up to lately, but I was just pointing out that they never jumped on the "borrowing variance" bandwagon for microarrays. The idea of borrowing variance is...
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