Forum: Bioinformatics
06-27-2016, 06:10 AM
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Replies: 1
Views: 7,613
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...
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Forum: RNA Sequencing
06-07-2016, 02:20 AM
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Replies: 0
Views: 1,252
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...
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Forum: Bioinformatics
02-19-2016, 11:10 AM
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Replies: 0
Views: 2,506
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Forum: Bioinformatics
10-23-2015, 03:27 AM
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Replies: 1
Views: 1,247
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...
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Forum: Bioinformatics
09-09-2015, 04:12 AM
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Replies: 1
Views: 916
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...
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Forum: RNA Sequencing
07-06-2015, 02:48 AM
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Replies: 0
Views: 897
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Forum: Bioinformatics
02-04-2015, 03:45 AM
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Replies: 123
Views: 50,455
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...
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Forum: Bioinformatics
02-03-2015, 08:07 AM
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Replies: 123
Views: 50,455
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Forum: Bioinformatics
02-03-2015, 07:34 AM
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Replies: 123
Views: 50,455
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...
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Forum: Bioinformatics
02-03-2015, 04:49 AM
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Replies: 123
Views: 50,455
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...
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Forum: Bioinformatics
12-01-2014, 08:04 AM
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Replies: 4
Views: 2,872
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:...
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Forum: Bioinformatics
09-23-2014, 04:59 AM
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Replies: 0
Views: 1,001
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 <-...
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Forum: Bioinformatics
07-18-2014, 07:15 AM
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Replies: 4
Views: 1,555
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Forum: Bioinformatics
07-02-2014, 03:45 AM
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Replies: 4
Views: 1,555
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...
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Forum: Bioinformatics
06-20-2014, 07:32 AM
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Replies: 123
Views: 50,455
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Forum: Bioinformatics
06-20-2014, 07:16 AM
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Replies: 123
Views: 50,455
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Forum: Bioinformatics
06-20-2014, 07:01 AM
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Replies: 123
Views: 50,455
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Forum: Bioinformatics
05-31-2014, 07:31 AM
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Replies: 2
Views: 4,350
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....
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Forum: Bioinformatics
05-22-2014, 07:27 AM
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Replies: 2
Views: 1,148
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...
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Forum: RNA Sequencing
04-11-2014, 08:56 AM
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Replies: 2
Views: 3,557
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Forum: Bioinformatics
04-05-2014, 05:51 AM
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Replies: 28
Views: 10,820
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Forum: RNA Sequencing
04-05-2014, 04:56 AM
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Replies: 2
Views: 3,557
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...
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Forum: Bioinformatics
03-26-2014, 05:36 AM
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Replies: 3
Views: 1,171
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Forum: Bioinformatics
03-20-2014, 05:13 AM
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Replies: 3
Views: 1,171
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...
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Forum: Bioinformatics
11-22-2013, 03:54 AM
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Replies: 6
Views: 8,085
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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