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Recent Replies
Comment: How to regress out age and sex using limma removeBatchEffect
by
aropri
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80
thank you, this worked. Appreciate your help so much.
Answer: How can I find a DNA sequence that codes for a protein from a large FASTQ file?
by
cmdcolin
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2.1k
FASTQ files are generally raw reads, and you would not generally look for protein sequences from these raw reads. Possible reasons: short r…
Comment: How to regress out age and sex using limma removeBatchEffect
by
aropri
▴
80
Will check that out. However, since this is proteomic expression, variance stabilized transformation is not the correct way to normalize th…
Comment: How to regress out age and sex using limma removeBatchEffect
by
aropri
▴
80
Thank you for your help, I used covariates but was only able to regress out one variable. Will try the method you advised and also check co…
Comment: How to regress out age and sex using limma removeBatchEffect
by
linnaeusbundalian
•
0
Do you need the corrected assay? cause the removeBatchEffect affects only the assay for the visualization hence you need to extract it from…
Answer: How to regress out age and sex using limma removeBatchEffect
by
Gordon Smyth
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4.4k
You just use `removeBatchEffect` with `batch = sex`, `covariates = age` and `design = design`.
Since you are already familiar with the `co…
Comment: How to regress out age and sex using limma removeBatchEffect
by
aropri
▴
80
I tried that and it computes but I feel like its not correct because it is giving me many values of infinity. Is there a way to use the cov…
Comment: How to regress out age and sex using limma removeBatchEffect
by
aropri
▴
80
so would first batch be batch = nph_csf_metadata$age, and second batch2 = nph_csf_metadata$sex?
Comment: How to access the ACLAME server?
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GenoMax
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This appears to be a 10+ year old paper and as with many of these services it may be dead. Are you certain it was available recently?
Answer: How can I find a DNA sequence that codes for a protein from a large FASTQ file?
by
GenoMax
115k
I will add one more idea. Once you get the DNA sequence of the protein you are looking for you can align (using a NGS data aligner) the rea…
Answer: How to regress out age and sex using limma removeBatchEffect
by
linnaeusbundalian
•
0
afaik, limma::removeBatchEffect can accept two batches i.e specifying batch = (first batch) and batch2 = (second batch)
Answer: How can I find a DNA sequence that codes for a protein from a large FASTQ file?
by
Mensur Dlakic
★
18k
I think most people on this forum will tell you that you should solve your homeworks independently. That is the whole point of learning, an…
Comment: How to add the ancestral allele (AA) information in a vcf file?
by
Pierre Lindenbaum
145k
no, unless you have file similar to http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/
Comment: How to add the ancestral allele (AA) information in a vcf file?
by
taniamahmood38
▴
20
Thanks for the help. But please kindly clarify that if the vcfancestralallele command will work on any specie vcf file other than human?
…
Comment: Lasso regression and cross-validation on RNA seq dataset
by
Mensur Dlakic
★
18k
Yes, the idea is to perform CV on a train dataset and evaluate on test. For this to be reliable, some kind of a stratified split is needed …
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