User: Pin.Bioinf

gravatar for Pin.Bioinf
Pin.Bioinf150
Reputation:
150
Status:
Trusted
Location:
Malaga
Last seen:
13 hours ago
Joined:
1 year, 4 months ago
Email:
i*************@gmail.com

Im a Health Engineer with a Bioinformatics specialization doing epigenetics research.

Posts by Pin.Bioinf

<prev • 81 results • page 1 of 9 • next >
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lncPath deleted from CRAN
... Hello, A few months ago I was using lncPath in order to find pathways for lncRNAs by association of these lncRNAs to protein coding genes by association in networks. This was a good package, but it has been deleted due to removal of another package 'samr' which was one of the options of significan ...
R lncrnas networks written 15 hours ago by Pin.Bioinf150 • updated 14 hours ago by zx87545.0k
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Comment: C: 25 DE genes with 8 samples and 4 DE genes with 16 samples
... Thank you for all your help ...
written 6 days ago by Pin.Bioinf150
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Comment: C: 25 DE genes with 8 samples and 4 DE genes with 16 samples
... It does not seem like there is a difference as good and bad samples do not appear even close to each other, so I think the reason i dont get any DE genes is because there are none that are significant enough. But as I am new to this and the biologist is saying that there is no way there are no DE ge ...
written 6 days ago by Pin.Bioinf150
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Comment: C: 25 DE genes with 8 samples and 4 DE genes with 16 samples
... ![PCA with batch info][1] [here][2] ![PCA without batch info ][3] [here][4] [1]: https://ibb.co/evdnUz [2]: https://ibb.co/evdnUz [3]: https://ibb.co/dchswe [4]: https://ibb.co/dchswe ...
written 6 days ago by Pin.Bioinf150
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Comment: C: 25 DE genes with 8 samples and 4 DE genes with 16 samples
... Yes, I did. By adding the batch information to the formula I only get 1 DE gene now! ...
written 6 days ago by Pin.Bioinf150
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Comment: C: 25 DE genes with 8 samples and 4 DE genes with 16 samples
... You mean add the batch parameter to the formula? Is that enough to solve batch effect? ...
written 6 days ago by Pin.Bioinf150
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25 DE genes with 8 samples and 4 DE genes with 16 samples
... Hello, I am doing a differential expression analysis, and first my group sequenced 8 samples of responders and non responders to a treatment, and asked that I analyze and get the DE genes (25 DE genes). After that, they sequenced 8 samples more, and now we get 4 DE genes, no gene matches the DE gen ...
deseq2 rna-seq written 6 days ago by Pin.Bioinf150 • updated 1 day ago by Biostar ♦♦ 20
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Comment: A: Good mean coverage but big std in coverage
... This is the table of some of the samples after mapping: Sample Name % Aligned M Aligned I_S1 4.7% 1.0 I_S2 48.7% 3.2 I_S3 49.0% 3.0 I_S4 46.6% 7.6 I_S6 82.4% 49.3 ...
written 10 days ago by Pin.Bioinf150
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Comment: A: Good mean coverage but big std in coverage
... Hello Corentin, thank you for your detailed answer. Then, looking at the % of uniquely mapped reads should be enough? How can I decide if the percentage of uniquely mapped reads is good enough for analysis? ...
written 10 days ago by Pin.Bioinf150
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Comment: C: Good mean coverage but big std in coverage
... So how do i know if my fastq file is good enough for differential expression analysis? This sample mapped 4,7% of reads against reference ...
written 10 days ago by Pin.Bioinf150

Latest awards to Pin.Bioinf

Supporter 11 days ago, voted at least 25 times.
Scholar 14 days ago, created an answer that has been accepted. For A: STAR --quantMode GeneCounts function
Autobiographer 16 months ago, has more than 80 characters in the information field of the user's profile.

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