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Forum: Bioinformatics 06-27-2016, 06:10 AM
Replies: 1
Views: 7,613
Posted By IsBeth
pheatmap with predefined row order (?)

Hello!

I used the pheatmap function (package pheatmap), an excellent function to obtain a heatmap of my top20 genes. But rows have to be shown within the heatmap in a specific order.

Now my...
Forum: RNA Sequencing 06-07-2016, 02:20 AM
Replies: 0
Views: 1,252
Posted By IsBeth
DESeq2 pheatmaps

Hi all,

I'm examining functions to create heatmaps so that I can show the expression pattern of the top of my differentially expressed genes list, but I am a bit confused about which data...
Forum: Bioinformatics 02-19-2016, 11:10 AM
Replies: 0
Views: 2,506
Posted By IsBeth
Too high adjusted P-values analysing RNA-seq count data with limma

Hello!

I'm trying to analyse an RNA-seq count data matrix with limma. From an input table with about 15000 entries, limma gets 1600 differentially expressed genes. That is OK, but these genes have...
Forum: Bioinformatics 10-23-2015, 03:27 AM
Replies: 1
Views: 1,247
Posted By IsBeth
Enrichment GO analysis with R on an ordered list

Hello all!

I'm trying to perform a gene set enrichment analysis from RNA-seq data on an ordered gene list, that is, a gene list with logFC or p-values. I want the analysis to get into account not...
Forum: Bioinformatics 09-09-2015, 04:12 AM
Replies: 1
Views: 916
Posted By IsBeth
LFCSeq Package

Hello!

I was trying to download the LFCSeq R-package to perform its non-parametric analysis on my data. But it seems it is not available for R-version 3.1.3. Is there any news if this package will...
Forum: RNA Sequencing 07-06-2015, 02:48 AM
Replies: 0
Views: 897
Posted By IsBeth
topGO error

Error solved =))
Forum: Bioinformatics 02-04-2015, 03:45 AM
Replies: 123
Views: 50,455
Posted By IsBeth
Hi Michael, You were absolutely right :) I...

Hi Michael,

You were absolutely right :) I had filtered the object returned from the results() function with a minimum log2foldChange of 1.5 and an adjusted p-value of 0.01. It was definitively...
Forum: Bioinformatics 02-03-2015, 08:07 AM
Replies: 123
Views: 50,455
Posted By IsBeth
Ok, so when estimating the variance this way, it...

Ok, so when estimating the variance this way, it is not sufficient to detect DE genes?:eek: I know that to work with no replicates is not appropiate, but in these cases I need to provide some...
Forum: Bioinformatics 02-03-2015, 07:34 AM
Replies: 123
Views: 50,455
Posted By IsBeth
Yes, I did. And I'm sorry, since I've seen that...

Yes, I did. And I'm sorry, since I've seen that this problem is treated in other posts (such as "DESeq2 without biol replicates"). I tried the following code, but it doesn't work by now (I need to...
Forum: Bioinformatics 02-03-2015, 04:49 AM
Replies: 123
Views: 50,455
Posted By IsBeth
Hello! I'm trying DESeq2 with synthetic...

Hello!

I'm trying DESeq2 with synthetic RNA-seq count data without replicates (40% of the synthetic genes are differentially expressed (DE), with a up - and downregulation ratio of 50%). Although...
Forum: Bioinformatics 12-01-2014, 08:04 AM
Replies: 4
Views: 2,872
Posted By IsBeth
Same error...

Hello!

I know this thread is a little bit old but I've got the same error with compcodeR now. The installation seems to work well, but when I try to load the library the following error appears:...
Forum: Bioinformatics 09-23-2014, 04:59 AM
Replies: 0
Views: 1,001
Posted By IsBeth
R - package sRAP

Hello! I'm trying out the sRAP package for R. I thought it would be very easy to implement but I get an error with the RNA.norm function when I try to use my own data:

expression.mat <-...
Forum: Bioinformatics 07-18-2014, 07:15 AM
Replies: 4
Views: 1,555
Posted By IsBeth
Thank you very much, all of you! I think...

Thank you very much, all of you!

I think your advices and links will help me a lot :)
Forum: Bioinformatics 07-02-2014, 03:45 AM
Replies: 4
Views: 1,555
Posted By IsBeth
Mathematical fool

Hello!

Well my problem is that I'm a Biologist and so I've got no much statistical or mathematical background to understand some procedures in R. (I'm working in differential expression of RNA-seq...
Forum: Bioinformatics 06-20-2014, 07:32 AM
Replies: 123
Views: 50,455
Posted By IsBeth
I'm reading your paper now. I will post my MA...

I'm reading your paper now. I will post my MA plot and ask more as soon I've read it. Thank you for your reply and for the link of your paper! =)
Forum: Bioinformatics 06-20-2014, 07:16 AM
Replies: 123
Views: 50,455
Posted By IsBeth
In my MAplot are differential expressed genes (in...

In my MAplot are differential expressed genes (in red). Yes, there are also negative values. I think I don't understand the concept of shrunken fold changes, still a newbie :o

It just seemed...
Forum: Bioinformatics 06-20-2014, 07:01 AM
Replies: 123
Views: 50,455
Posted By IsBeth
Hello, I'm using DESeq2 and so far it seems...

Hello,

I'm using DESeq2 and so far it seems to work well. But why are the log fold changes so low? They have values between 0 and 1, even when the genes are differentially expressed.
Forum: Bioinformatics 05-31-2014, 07:31 AM
Replies: 2
Views: 4,350
Posted By IsBeth
Getting normalized counts

Hello,

I've tried to find differential expression with edgeR and DESeq2. These packages normalize my count data first, but they do not automatically provide normalized read counts to the end user....
Forum: Bioinformatics 05-22-2014, 07:27 AM
Replies: 2
Views: 1,148
Posted By IsBeth
Rename whole data sets

Hello! Sorry if my question seems a bit stupid, cause I think it has to be easy, but I don't have enough knowhow...
I want to rename a character string in R which contains numbers. It's something...
Forum: RNA Sequencing 04-11-2014, 08:56 AM
Replies: 2
Views: 3,557
Posted By IsBeth
Thank you! I think I will have to wait a few days...

Thank you! I think I will have to wait a few days then, but no problem ^^
Forum: Bioinformatics 04-05-2014, 05:51 AM
Replies: 28
Views: 10,820
Posted By IsBeth
Hi! I've got a similar problem with plotMA...

Hi!

I've got a similar problem with plotMA in DESeq2. Here is my session info:

R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1]...
Forum: RNA Sequencing 04-05-2014, 04:56 AM
Replies: 2
Views: 3,557
Posted By IsBeth
Question DESeq2 for R-version 3.1?

Hello,

I've updated my version of R today from 3.0.2 to 3.1. Now when I'm trying to install DESeq2, I get a warning message like this:

Warning in install.packages :
package ‘DESeq2’ is not...
Forum: Bioinformatics 03-26-2014, 05:36 AM
Replies: 3
Views: 1,171
Posted By IsBeth
Thank u dpryan. The table-function worked =) ...

Thank u dpryan. The table-function worked =)

What if I wanted to use a function like that with my counts, not with my design table? A data frame like this for example:

Control1 Control2 ...
Forum: Bioinformatics 03-20-2014, 05:13 AM
Replies: 3
Views: 1,171
Posted By IsBeth
Question Looking for replicated conditions

Hello! I'm a newbie and I'm trying to write a function which can read how much replicated conditions there are in an experimental design in a given case. For example, if I have a design (for example...
Forum: Bioinformatics 11-22-2013, 03:54 AM
Replies: 6
Views: 8,085
Posted By IsBeth
My pipeline in DEseq using data without...

My pipeline in DEseq using data without replicates and 2 conditions is not working either. I thought that something was wrong with the dispersion. But no dispersion method works, so...maybe there's a...
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