Hi,
I used a tool to perform differential expression analysis on my microarray data sets,
The output is something like below
ProbesetID logFC AveExpr t P.Value adj.P.Val B
1769308_at 1.89394112596704 10.5871328585202 16.4749776727376 3.68669391559684e-10 2.6623530112e-08 13.7014616531283
1769311_at -0.115715211915935 10.5999601204582 -1.12002479223092 0.282752344869474 0.382582735789368 -7.1722215976202
1769312_at 0.131966902231916 9.02503563963962 1.5364411821642 0.148147122010043 0.230066458270885 -6.6497072352879
Sorry, may someone please tell me how I can select only the probsets with a desire fold change or P.Value?
For example probesets more than 1
Thank you so much
2 answers
In R, take a look at the help for subset().
Did you read the help for subset by typing help("subset")? Notice that the help for R functions usually includes one or more examples at the end of the help page which you should read and type into R by hand. Also, a quick google search turns up: http://www.r-bloggers.com/subsetting-data/ and http://www.ats.ucla.edu/stat/r/modules/subsetting.htm among many others. If this doesn't help, then I would advise an online course in R before proceeding, as subsetting is a basic necessity for doing any work in R.
•
written
by
Sean Davis
I assume the above output is from topTable, right?
for instance(assuming that my above notion is correct)--as you have a data.frame, let's called it dat, which has the output of topTable. Then, you could use something like the following:
dat2 <- dat[which(abs(dat$logFC) >cutoff1 & dat$adj.P.Val < cutoff2),] # in order to satisfy both cutoff1 and 2-where the two cutoffs depend on the user
Hope that helps,
Efstathios
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written
by
svlachavas
then first thing you spend your time on is R.
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written
by
Sukhi Singh
This can go in wrong direction, why not learn R?
actually you all right, but one month more I should leave Germany while I don't have any result to defend my dissertation. you can't imagine how much I am worry and concentrate on anything and only I am trying to collect some results...never I thought the final of my studying here would be like this... :(
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