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Recent Replies
Answer: comparisons between 2 ChIP-seq datasets
by
ATpoint
60k
You do not have any replication, hence you cannot make any meaningful statistics, nor can you make statements about the range of noise the …
Comment: How to access the ACLAME server?
by
cloredana20
•
0
Yes. The last time I accessed this server was in February this year. Do you know of any similar database? I need a server to characterize s…
Comment: How to add the ancestral allele (AA) information in a vcf file?
by
taniamahmood38
▴
20
Okay but I dont have this file so is there any other way to do that? Kindly let me know, thank you
Answer: How to do RNA-Seq metadata analysis?
by
seidel
9.4k
I think you'll have to explore your data, and make decisions based on the questions you have, and what it is you're trying to determine. Ma…
Answer: pfam functional redundancy
by
Mensur Dlakic
★
18k
There will be a lot of redundancy, which is why families are grouped into clans. Yet the main cause redundancy may not be what you assumed …
Comment: How can I find a DNA sequence that codes for a protein from a large FASTQ file?
by
Mensur Dlakic
★
18k
> FASTQ files are generally raw reads, and you would not generally look for protein sequences from these raw reads.
It is a class project,…
Comment: How to regress out age and sex using limma removeBatchEffect
by
aropri
▴
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
★
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
machan
•
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
★
4.4k
You just use `removeBatchEffect` with `batch = sex`, `covariates = age` and `design = design`.
As the help page `?removeBatchEffect` explai…
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?
by
GenoMax
115k
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?
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