User: Marie

gravatar for Marie
Marie0
Reputation:
0
Status:
New User
Last seen:
4 years, 1 month ago
Joined:
4 years, 2 months ago
Email:
p*************@hotmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by Marie

<prev • 8 results • page 1 of 1 • next >
0
votes
5
answers
2.5k
views
5
answers
Answer: A: Intepretation of RUVseq/edgeR logFC
... Ok thank you so much, it is clear now !! Yes I know that 11 genes are way too few, we are working on making a longer list. I tried to compute RUVg with k=2 and I have filtered the genes which the expression is lower than 10, and I don't have weird fold change anymore. On the contrary, they are pre ...
written 4.2 years ago by Marie0
0
votes
5
answers
2.5k
views
5
answers
Answer: A: Intepretation of RUVseq/edgeR logFC
... Ok thanks a lot for your answer. I tried to do the log 2 ratio of fitAD$coefficients but I don't find the same value as logFC. I surely miss something here... I would like to have these "2 values" just to show where the logFC comes from, as I have for the FPKM analysis, to make things clearer for ...
written 4.2 years ago by Marie0
0
votes
7
answers
1.2k
views
7
answers
Answer: A: RUV: removing unwanted variation in RNA-seq
... Ok I think you did well ! I'm glad if it works now. Best ...
written 4.2 years ago by Marie0
0
votes
7
answers
1.2k
views
7
answers
Answer: A: RUV: removing unwanted variation in RNA-seq
... Can you show the result of "head(genes)" please ? Are you sure all your genes names start by "ENS" ?   ...
written 4.2 years ago by Marie0
0
votes
5
answers
2.5k
views
5
answers
Comment: C: Intepretation of RUVseq/edgeR logFC
... Ok I'm not sure of what prior count really means... I need to have the 2 values that are used to calculate the logFC in my output but I just can't figured out how I can find them, any ideas ? Thank you ! ...
written 4.2 years ago by Marie0
0
votes
7
answers
1.2k
views
7
answers
Answer: A: RUV: removing unwanted variation in RNA-seq
... Hi, I recently started to use RUV-seq too. I'm not sure if I understand well your first question but the ERCC spikes have to be spiked into the RNAseq mix before sequencing. You can try using housekeeping genes as controls.   For you error messages, could you tell us how you defined your 'set' ...
written 4.2 years ago by Marie0
0
votes
5
answers
2.5k
views
5
answers
Answer: A: Intepretation of RUVseq/edgeR logFC
... Thank you very much for your helpful answer. I will try to repeat the analysis without the estimated RUV factors as you suggest. In my current results, I can see a logFC=18 for a gene which has raw counts like 0,1,8 vs 2,1,4 so I really don't get how it calculates the logFC. It computes a ratio of ...
written 4.2 years ago by Marie0
1
vote
5
answers
2.5k
views
5
answers
Intepretation of RUVseq/edgeR logFC
... Dear All, I'm working on a genomic plateform and I'm in charge of analysing biological data. A team of researchers asked me to compare two different methods to compute differentially expressed genes in a given dataset, from illumina human RNAseq data, aligned with Tophat2. My dataset in composed o ...
edger ruvseq logfc written 4.2 years ago by Marie0

Latest awards to Marie

Popular Question 4.2 years ago, created a question with more than 1,000 views. For Intepretation of RUVseq/edgeR logFC

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 164 users visited in the last hour