User: Hayssam

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Hayssam270
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France
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4 years, 9 months ago
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6 years, 5 months ago
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Posts by Hayssam

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Any Tutorial For Co-Expression(Network) Analysis?
... Last time was with 400 samples (time course RNA-Seq). ...
written 5.4 years ago by Hayssam270
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Answer: A: David Upload Background Problem
... Hi, There's a limitation in DAVID with regards to custom background and gene symbol. I think it has to do with the impossibility to distinguish species based on gene symbol alone. For the backgrounds, you have to provide e.g. ENSEMBL gene ID, ENTREZ gene ID or probe ID; depending on how your back ...
written 5.4 years ago by Hayssam270
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Comment: C: How To Find Differentially Expressed Transcripts Across Tissues?
... Yep it does make things clearer! Do you have replicates? Or can you group the tissues so as to have more degrees of freedom? ...
written 5.4 years ago by Hayssam270
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Comment: C: How To Find Differentially Expressed Transcripts Across Tissues?
... The word "pattern" is used a bit too liberally for me to grasp what you mean, sorry :( But I think I understood what you're after: Not differential expression per se, but more to answer questions of they type " Is transcript A the reference transcript in all tissues?", where reference transcript is ...
written 5.4 years ago by Hayssam270
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Answer: A: Driver And Passenger Mutations In Cancer
... Hi, to follow up a bit on Chris' answer, I would add a semantic twist to your question: Short answer : Use databases indicating whether a mutation can be a driver, e.g. COSMIC etc. intermediate answer : You can't answer your question just by observation Long answer : You can determine whether ...
written 5.4 years ago by Hayssam270
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Comment: C: Comparing Rpkms For One Test Sample Vs Multiple Controls
... Different library sizes (due to both different sequencing depth and different ratio of mappable reads) are exactly the raison d'être for these approaches. There's several papers explaining why RPKM is not appropriately dealing with that. See e.g. Damian's answer and this thread. About RPKM inconsis ...
written 5.4 years ago by Hayssam270
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Answer: A: Comparing Rpkms For One Test Sample Vs Multiple Controls
... Hi, I don't think there's any reason not to start by using one of the available differential expression test in R. I'd recommend edgeR or DESeq. Both have nice tutorials to get you started and both should handle the class imbalance adequately. However these two methods expect raw reads counts, not ...
written 5.4 years ago by Hayssam270
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Comment: C: How To Find Differentially Expressed Transcripts Across Tissues?
... That's an interesting question, although I couldn't manage to exactly figure what you are after. The notion of "pattern" would require some definition I think. If the reference transcript of a protein is highly expressed in a single tissue, and not expressed at all in the others, would it be a hit? ...
written 5.4 years ago by Hayssam270
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Comment: C: Pubmed Entrez Data
... I don't see the discrepancies about this articles. If you look at the MEDLINE records : http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=24016960,24016983,24017236&retmode=MEDLINE&rettype=MEDLINE The EDAT corresponds to the pubstatus="pubmed" node. Did I miss someth ...
written 5.4 years ago by Hayssam270
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Comment: C: Pubmed Entrez Data
... I think these articles are indicated as being under processing. Can you give some PUBMEDID examples of these? ...
written 5.4 years ago by Hayssam270

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Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: How To Compare Raw Counts From Rnaseq ?

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