User: mforde84

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mforde84490
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Posts by mforde84

<prev • 113 results • page 1 of 12 • next >
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Comment: C: Quick question about analysis of log2 RMA data
... If I understand correctly the resulting fold change is still in log2, correct? So 0.5 is not actually double the intensity of 0.25, where 2 = 0.5 / 0.25. But instead 1.19x because 2^(0.5-0.25). And 2^( (0.5-0.25) / 0.25) doesn't make sense because log2 isn't linear. ...
written 13 days ago by mforde84490
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Quick question about analysis of log2 RMA data
... Say I have some probe level and RMA normalized array data. The data is supposedly log2 normalized already. How do I calculate the relative difference in intensity between two probes? If I understand correctly, it should just be the 2^residual. For example probe1 = 1 probe2 = 2 2^(2- ...
microarray written 13 days ago by mforde84490
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Comment: C: STAR alignment, RNA-seq
... For posterity sake, take a handful of the unmapped reads and blastn them. ...
written 26 days ago by mforde84490
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Comment: C: cross strand correlation in BrU-UV ChIP data
... Really would appreciate some help with this. Thanks. ...
written 27 days ago by mforde84490
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Comment: C: SNP analysis based on RNAseq data using GATK PIPELINE
... From some limited experience with variant calling on RNAseq data, I'm not entirely sure base score recalibration adds a whole lot to the sensitivity and specificity of the calls. Indel realignment just seems like a good idea, imo. Though the question I think is a bit moot anyway. If you have the com ...
written 27 days ago by mforde84490
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Comment: C: SNP analysis based on RNAseq data using GATK PIPELINE
... Depends. Typically thats something you'll need to research. http://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set ...
written 28 days ago by mforde84490
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Answer: A: SNP analysis based on RNAseq data using GATK PIPELINE
... That would be a deletion of ACTTGG, and if the columns were reversed it would be an insert. ...
written 28 days ago by mforde84490
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Comment: C: how to visualize the distribution of 20,000 genes in gene expression data
... I don't know if you're better off heatmapping a quarter million data points though, especially if you're not scaling the data for each gene. Maybe visual examination is out of the question. Instead iterate through each gene, and do a shapiro test for each to assess normality: > shapiro.test(y)$ ...
written 28 days ago by mforde84490
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Answer: A: Creating the gene sets for GSEA in R
... Try using EGSEA instead (http://bioconductor.org/packages/release/bioc/html/EGSEA.html). You can generate geneset lists using: buildKEGGIdx, buildMSigDBIdx, etc. ...
written 28 days ago by mforde84490
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Answer: A: Help with Samtools
... I think this should work so long as the sam file has headers: samtools view -Sb file.sam | samtools sort -n - file.sort ...
written 28 days ago by mforde84490

Latest awards to mforde84

Scholar 28 days ago, created an answer that has been accepted. For A: SNP analysis based on RNAseq data using GATK PIPELINE
Scholar 28 days ago, created an answer that has been accepted. For A: SNP analysis based on RNAseq data using GATK PIPELINE
Centurion 10 weeks ago, created 100 posts.
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Heatmaps: Why and How to use them
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Heatmaps: Why and How to use them
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics in a clinical diagnostic setting versus research (academia)
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Heatmaps: Why and How to use them
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Heatmaps: Why and How to use them

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