User: lmolla

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lmolla10
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United States
Last seen:
3 months ago
Joined:
3 years, 1 month ago
Email:
l*****@rockefeller.edu

Posts by lmolla

<prev • 8 results • page 1 of 1 • next >
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Answer: A: motifStack importMatrix problem reading meme file to pcm
... Well I solved this by doing the following:   for (i in 1:length(motifs)){ motifs[[i]]@mat =motifs[[i]]@mat[,1:ncol(motifs[[i]]@mat)-1] } ...
written 3 months ago by lmolla10
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motifStack importMatrix problem reading meme file to pcm
... I am trying to import my list of motifs (that were output of MEME) motifs<-importMatrix(file),                      format="meme",                       to="pcm") When I look at the result there is one more extra column than what I expect with an A value of 'NA'; the motif is only 8 bases long ...
motifstack meme written 3 months ago by lmolla10 • updated 3 months ago by Ou, Jianhong1.1k
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Comment: C: Error in GRanges: could not find symbol "recursive" in environment of the generi
... any solutions if I have Mac OS X 10.9 (Mavericks) ; can not update R in this case ...
written 8 months ago by lmolla10
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Comment: C: DEseq2 time-series design.
... I am sorry to bother you again but when I run the design above I get :  > resultsNames(dds) [1] "Intercept"                    "time_d1_vs_d0"                "time_d2_vs_d0"                [4] "condition_KD_vs_control" "timed1.condition.KD"      "timed2.condition.KD" I want to be able to produc ...
written 3.1 years ago by lmolla10
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Comment: C: DEseq2 time-series design.
... Thank you very much for your reply!    ...
written 3.1 years ago by lmolla10
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Comment: C: DEseq2 time-series design.
... Hi Michael, Thank you very much for your reply and for being so helpful. My experiment is a bit more complicated but I am indeed interested in changes at time0 as well.   I have a time course experiment and I am also interested in differences at time0. My variables are :  condition=wt and knockdo ...
written 3.1 years ago by lmolla10
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Answer: A: DEseq2 time-series design.
... Hi cshao  ,  I am doing a similar analysis. Can you write the final code that you decided to use here.  I am specifically interested in the design.  From what I understand the better model to use is :   full = formula(~ Time + Treat + Time:Treat), reduced = formula(~ Time) From this test the ge ...
written 3.1 years ago by lmolla10
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Comment: C: DESeq2 baseMean values for each sample
... I had a similar question and I ran the code on my data (3 samples= x,y,z, 3 time points= day0,day1day2, so 9 combinations in total) unfortunately when look at the baseMean data all the output is NA.                                   day0 - x day0 - y day0 - z day1 - x day1 - y day1 - z day2 - x day ...
written 3.2 years ago by lmolla10

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