User: elb
elb • 110
- Reputation:
- 110
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Posts by elb
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0
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1
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... Hi guys,
could you suggest me a way to normalize Illumina expression beadchip data?
For example, starting from the `GSE32025_non-normalized.txt.gz` file, could you suggest me some few steps (preferentially in R) to finally obtain a normalized data matrix as for Affymetrix RMA normalisation? I sup ...
written 2 days ago by
elb • 110
• updated
2 days ago by
Kevin Blighe ♦ 28k
4
votes
1
answer
67
views
1
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... Hi guys,
I have a question about how to choose a reasonable threshold to define genes to be expressed (not differentially expressed but simply expressed) to compare gene expression measurements from different platforms. In other words I have to check if my list of genes is expressed using an RNA se ...
written 5 days ago by
elb • 110
• updated
5 days ago by
Devon Ryan ♦ 84k
0
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235
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Comment:
C: FeatureCounts on HG38
... Successfully assigned reads is different ...
written 9 weeks ago by
elb • 110
4
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0
answers
235
views
7 follow
0
answers
... Hi guys,
I'm trying to move from HG19 to HG38. While running FeatureCounts using Refseq*.gtf I see some differences between HG19 and HG38. This I suppose is expected but I only would like to know if I'm doing wrong since I'm a newbie in the RNA-Seq HG38 analysis. Here some outputs of FeatureCounts ...
0
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197
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1
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... It is fantastic! It works perfectly. Thank you very very much!
...
written 9 weeks ago by
elb • 110
7
votes
1
answer
197
views
6 follow
1
answer
... Hi guys,
I have a folder with around 300 `.bam` files. Each `.bam` file is a lane of a sample and hence 4 lanes make a sample. I would like to merge the .bam files of the four lanes in a single one by `_*S*_` where S is followed by a number that represent the number of the sample (e.g. `my_experime ...
written 9 weeks ago by
elb • 110
• updated
9 weeks ago by
WouterDeCoster ♦ 32k
0
votes
1
answer
208
views
1
answers
Comment:
C: RNA-Seq error in htseq-count
... So basically I'm doing some naive mistakes...I try to run properly. Thank you very much. ...
written 10 weeks ago by
elb • 110
2
votes
1
answer
208
views
1
answer
... Hi guys, I really do not know what is happening to my RNA seq data analysis pipeline and hence I'm looking for some help.
Although I found some related posts and I tried to follow instructions to solve the problem I'm still here and I'm getting crazy.
Briefly: the steps are the following:
# STA ...
0
votes
0
answers
232
views
0
answers
... I have no idea...I used the mutual information in the past but with 300 samples... ...
written 5 months ago by
elb • 110
1
vote
0
answers
232
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0
answers
... Guys,
I have 5 samples (patients) and around 12.000 expressed genes. I would like to predict some interactions (networks) among that genes in terms of gene expression in each sample and across the samples. My question is: due to the small sample size, is there some statistic or some algorithm for t ...
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