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Recent Replies
Comment: microarray analysis in R
by
bioinformatics
▴
10
Ok thanks, how do I easily create a character vector with over 12,000 probe names?
Comment: Check barcode collision
by
Vincent Laufer
★
2.4k
nice 1 jesse. another alternative could be functionality built into seurat4.
vl
Answer: Check barcode collision
by
Jesse
▴
200
1733 lines isn't very much, but it's doing a lot of comparisons between those with the same steps over and over, so I'd say load the whole …
Answer: Any option in bwa mem aligner for headless sam output?
by
Pierre Lindenbaum
149k
bwa me r.fa R1.fq.gz R2.fq.gz | grep -v '^@SQ'
Comment: converting probes robes to gene IDs
by
ATpoint
65k
Google it or use the search function. As said before, these array questions have been asked extensively over the last decade. Show effort a…
Comment: -bash efetch command not found
by
ÖZGÜN
•
0
Thank you for advice but unfortunately, I wrote the script (efetch -db=nuccore -format=fasta -id=AF086833 > AF086833.fa) according to, "The…
Comment: -bash efetch command not found
by
ÖZGÜN
•
0
Thank you for your advice.
When I try to script the code (sudo chown ozgun ~/.bash_profile chmod +w ~/.bash_profile) I got this message.
ch…
Comment: microarray analysis in R
by
Kevin Blighe
83k
Okay. Please re-check what I wrote. The variable, `probes`, must contain the probe IDs from your experiment - it should be a character vect…
Comment: How I do lift over a Plink bim file from Hg18 to Hg19.
by
yas
•
0
Just got a similar issue and it seems that the liftOverPlink script can't execute the liftOver binary file. You need to change the permissi…
Comment: microarray analysis in R
by
bioinformatics
▴
10
Ok thanks for your insight! When I use the command:
annotLookup <- select(hgu133a.db, keys = probes,
columns = c('PROBEID', 'EN…
Answer: converting probes robes to gene IDs
by
Kevin Blighe
83k
I have answered you here: https://www.biostars.org/p/9539504/#9539527
Comment: microarray analysis in R
by
Kevin Blighe
83k
You can create an annotation lookup table for this array for your probe IDs, held in `probes`, via:
require(hgu133a.db)
annotLooku…
Comment: microarray analysis in R
by
Kevin Blighe
83k
Okay, they are all from the same study, which utilised the Affymetrix U133A. I am guessing that your variable, `CelFiles`, contained non-CE…
Comment: batch download data from webpage https://www.hmpdacc.org/hmasm2/
by
Wen
•
0
I did have checked this page before. But it need an account for regestration, but the website is no longer mainteened. So it failed this wa…
Comment: Error with txi.salmon in R
by
rpolicastro
9.8k
Oh sorry, I didn't even notice that it quantified at the chromosome level. What code did you use to generate the transcriptome?
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