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Comment: microarray analysis in R
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bioinformatics
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Do you know if these commands are correct for a successful microarray differential analysis?
Comment: DE analysis with multiple factors
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Abhishek
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Thank you for the suggestion.
Merging the 2 factors seems to be a good approach.
However for comparison 1, env1 vs env2, is it okay to jus…
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More on the dots: [GenotypeGVCFs and the death of the do][1]
[1]: https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-Genotyp…
Answer: How to populate snp vcf file
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Istvan Albert
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You could use `bcftools` plugins:
https://samtools.github.io/bcftools/howtos/plugins.html
for example:
bcftools +setGT --help
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The same DNA template will be read several times as the image indicates. Since the adapters are known, these will be recognized by the soft…
Comment: DE analysis with multiple factors
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Abhishek
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Thank you for the response.
(As you suggested), so as not to exclude samples, cant I use the same limma based DEP package, but combine the …
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How was vitalStatus_cox coded? Assuming that death = 1 and censored = 0, this data shows that the risk associated with DEG is 0.93345 time…
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Chris
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@genomax Yes, I can view the header with:
samtools view -h MT1/Tophat_Out/accepted_hits.sorted.bam
It is a follow-up question in whic…
Comment: htseq-count: error when reading beginning of SAM/BAM file.
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Please use
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instead of the line you have.
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check your PATH https://linuxhint.com/path_in_bash/
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Wandered here from Google, a revision for others who land here:
The 'Simpler version' has a bug, it needs to reset `c=0` at each sequence h…
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Marco Pannone
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I would adjust `--zMax` based on the heatmap with the highest intensity among the ones to be compared. Plotting also a profile plot on the …
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jkim
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Sorry, I thought you didn't include the batch variable in the model :-)
Comment: Deeptools comparing heatmap zMin and zMax across different plotHeatmaps
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connorjfausto
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Hi Marco,
Thanks for the reply! So even if the visualization intensity comes from different matrix files, the intensity can be compared? W…
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