User: Aurelie MLB

gravatar for Aurelie MLB
Aurelie MLB290
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290
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Location:
United Kingdom
Last seen:
4 months ago
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3 years, 4 months ago
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Posts by Aurelie MLB

<prev • 64 results • page 1 of 7 • next >
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Comment: C: [Should I used CAGE?]: gene set enrichment analysis on image analysis experiment
... Thanks a lot! This is helpful. ...
written 4 months ago by Aurelie MLB290
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[Should I used CAGE?]: gene set enrichment analysis on image analysis experimental values
... Hello, I have experimental values for a large set of genes that are NOT coming from sequencing. They are image analysis derived GFP intensities. From these values, some of those genes are interesting and some are not so I could if needed define a set of "interesting" genes. But I would prefer to ta ...
gene pathway bioprocess written 4 months ago by Aurelie MLB290 • updated 4 months ago by Jean-Karim Heriche13k
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Comment: C: RNA-seq: how big should be the library?
... Hello, May I ask a stupid question please? I would like to double check. When someone talk about the "size of the library", does he means the number of forward reads PLUS the number of reverse reads? Or does he mean the number of templates (i.e. == Number of forward reads) please? ...
written 18 months ago by Aurelie MLB290
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Comment: C: Ideal size of a library for miRNA ?
... Thank you ! ...
written 20 months ago by Aurelie MLB290
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Ideal size of a library for miRNA ?
... Hello, I was wondering what is your experience about miRNA sequencing please? What would be the ideal size for a library? I found this documentation from Exiqon (http://www.exiqon.com/ls/Documents/Scientific/Service-Customer-Information-NGS.pdf) basically saying that 5 M reads should be sufficient ...
rna-seq written 20 months ago by Aurelie MLB290 • updated 20 months ago by Chris Fields1.8k
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Answer: A: DESeq2: why the independent filtering threshold would come back as NULL please?
... Hello, I have found the answer to my question. In the updated vignette, it is explained that the filtering threshold can be obtained by: metadata(RES)$filterThreshold. RES being what is returned by the "results" function. So I guess my code was out of date. Thanks ...
written 20 months ago by Aurelie MLB290
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Comment: C: Sailfish TPM normalization: does it take into account the size the library?
... Thank you very much! ...
written 20 months ago by Aurelie MLB290
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Comment: C: Sailfish TPM normalization: does it take into account the size the library?
... Thanks a lot for your explanation! ...
written 20 months ago by Aurelie MLB290
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Comment: C: Sailfish TPM normalization: does it take into account the size the library?
... Hello, Thanks a lot for your answer. Very helpful ! I did not know I could use the sailfish NumReads for differential expression analysis. I will have a closer look. Thanks! The first part of your answer is actually the type of explanation I was looking for. So, (please correct me if I am wrong) ...
written 20 months ago by Aurelie MLB290
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Sailfish TPM normalization: does it take into account the size the library?
... Hello, I apologize if it is a silly question. I am trying to get my head around the Sailfish TPMs. I can read in the paper that the "estimated abundances are corrected for systematic errors resulting from sequence composition bias and transcript length". But I cannot see anything about the size of ...
rna-seq written 20 months ago by Aurelie MLB290 • updated 20 months ago by Rob2.1k

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Popular Question 18 months ago, created a question with more than 1,000 views. For In R bioconductor, how to combine DNAString views please ?
Popular Question 20 months ago, created a question with more than 1,000 views. For How to link UCSC transcripts ids to protein ids using bioconductor ?
Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2 normalisation: is the size of the gene taken into account?
Good Question 2.0 years ago, asked a question that was upvoted at least 5 times. For RNA-seq: how big should be the library?
Supporter 2.3 years ago, voted at least 25 times.
Appreciated 2.4 years ago, created a post with more than 5 votes. For RNA-seq: how big should be the library?
Student 2.5 years ago, asked a question with at least 3 up-votes. For RNA-seq: how big should be the library?

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