User: Lana Schaffer

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Lana Schaffer1.3k
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Posts by Lana Schaffer

<prev • 129 results • page 1 of 13 • next >
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edgeR FC calculation question
... Hi, Can you please tell me how the FC is calculated in the following test in edgeR? DrugvsPlacebo.1h = (Drug.1h-Drug.0h)-(Placebo.1h-Placebo.0h), Lana Schaffer The Scripps Research Institute Biostatistics, Informatics DNA Array Core Facility 858-784-2263 [[alternative HTML version deleted ...
written 3.8 years ago by Lana Schaffer1.3k • updated 3.8 years ago by Ryan C. Thompson6.1k
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Comment: C: DESeq Fold-Change calculation
... Simon, Yes, I was incorrect in saying that the FC calculation used unnormalized values. I have been given 2 equivalent datasets (8 controls and 8 treated) and need to "Show 'concordant' or reproducible hits". Using DESeq, dataset B gave only 21 (set B) transcripts significant compared to 431 for ...
written 5.2 years ago by Lana Schaffer1.3k
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Comment: C: DESeq variance stabilization
... Steve, Thank you for your suggestion. However, the idea of these datasets Is to access the reproducability of the results. Lana -----Original Message----- From: Steve Lianoglou [mailto:mailinglist.honeypot@gmail.com] Sent: Sunday, August 26, 2012 5:18 AM To: Lana Schaffer Cc: bioconductor at r-pr ...
written 5.2 years ago by Lana Schaffer1.3k
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DESeq variance stabilization
... Hi, I have 2 RNAseq datasets which are the same experiment both having 8 control and 8 treated Samples. I found that they have slightly different standard deviation values and that the Results are different between the 2 datasets. The set with the lower standard deviation Gives a longer list of hi ...
rnaseq written 5.2 years ago by Lana Schaffer1.3k • updated 5.2 years ago by Steve Lianoglou12k
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DESeq Fold-Change calculation
... Hi, I haven't checked to see if there has already been a discussion about the fold-change Calculation in DESeq, but I have found that the fold-change is calculated using the Raw count values and not the normalized count values. I usually use the fold-change With a cutoff value, but this isn't va ...
deseq written 5.2 years ago by Lana Schaffer1.3k • updated 5.2 years ago by Simon Anders3.4k
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edgeR for miRNA
... Hi, Is the program for edgeR used for miRNA? Lana Schaffer Biostatistics, Informatics DNA Array Core Facility 858-784-2263 [[alternative HTML version deleted]] ...
edger written 6.0 years ago by Lana Schaffer1.3k • updated 6.0 years ago by Mark Robinson870
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Comment: C: uneven counts for edgeR
... Gordon, An unnamed company is claiming that the RPKM counts and/or Some transformation of the RPKM counts is 90% normal, 5% NB, And 5% poisson distribution using the Akaiki Information Criteria. Can you explain why this is or is not plausable? Lana -----Original Message----- From: Gordon K Smyth [ ...
written 6.1 years ago by Lana Schaffer1.3k
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RNA-Seq: lognormal, Neg Bin, Poisson distribution
... Hi, I have been told that using the AKIKE Information Criteria that the read counts for transcripts is 90% lognormal distribution, 5% negative binomial distribution, 5% Poisson Distribution. Where can I find information about this? What other information is there about this issue? Thanks, Lana Scha ...
written 6.1 years ago by Lana Schaffer1.3k
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Comment: C: uneven counts for edgeR
... Gordon, Thank you for this information. Is the same true for DeSeq? Lana -----Original Message----- From: Gordon K Smyth [mailto:smyth@wehi.EDU.AU] Sent: Saturday, October 22, 2011 5:42 PM To: Lana Schaffer Cc: Bioconductor mailing list Subject: uneven counts for edgeR Dear Lana, edgeR has no dif ...
written 6.1 years ago by Lana Schaffer1.3k
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PCR bias in RNA-Seq
... Hi, Do you have any recommendation to remove reads due to PCR bias in RNA-Seq? Lana Schaffer Biostatistics, Informatics DNA Array Core Facility 858-784-2263 [[alternative HTML version deleted]] ...
written 6.1 years ago by Lana Schaffer1.3k

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