User: lily

gravatar for lily
lily10
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11 months, 2 weeks ago
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2 years, 2 months ago
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Posts by lily

<prev • 22 results • page 1 of 3 • next >
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meta de r package
... Hi While performing meta analysis using Meta DE r package, is it required to do batch effects for the datasets? ...
meta analysis written 11 months ago by lily10
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differentially expressed miRNA from TCGA miRna seq data
... Hi Is it compulsory that differentially expressed mirna should be found only from matched samples (sequencing data from both normal and cancer tissue in the same patients) of TCGA data ?? Can i combine both matched as well as unmatched samples to find DEmirna? ...
tcga written 13 months ago by lily10
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differentially expressed miRNA
... Hi If i want to find the differentially expressed miRNA between normal and tumor samples, do i need to set contrast matrix?? ...
limma written 13 months ago by lily10 • updated 13 months ago by Aaron Lun21k
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RobustRankAggreg in R
... Hi I just try the example data in RobustRankAggreg in R. I got the error message like aggregateRanks(glist = glist, N = length(letters)) Error: could not find function "aggregateRanks" Please help!!! ...
R written 13 months ago by lily10
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differentially expressed genes form RSEM genes data
... Hi  I have level3 RSEM gene data with raw counts. I want to find the differentially expressed genes using edge R but the problem is raw counts seems to be non-integer. What steps should i follow to get DEGs? Thanks ...
rnaseq edger written 14 months ago by lily10 • updated 14 months ago by Gordon Smyth35k
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differentially expressed miRNA
... I have downloaded mirnaseq illumina hiseq level 3 data from TCGA. Now i have to find the DEmirna. So do i need to normalize the data again as found that level 3 is already normalized.  ...
normalization written 14 months ago by lily10
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Comment: C: differentially expressed miRNA using edge R
... Thanks.  ...
written 14 months ago by lily10
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Comment: C: differentially expressed miRNA using edge R
... Thanks for the reply. One more doubt, read counts and raw counts are the same. If i have the raw counts then can i used edge R to get DEmiRNA ?? ...
written 14 months ago by lily10
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differentially expressed miRNA using edge R
... hi i have downloaded miRNA-seq RPKM-log data from TCGA portal. If i want to find the differentially expressed miRNA , can i used directly RPKM data or do i need to change to CPM ??    ...
edger written 14 months ago by lily10 • updated 14 months ago by Gordon Smyth35k
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meta analysis using MetaDE
... Hi I have got the result like this > count.DEnumber(res1,p.cut=c(0.001,0.005),q.cut=c(0.01,0.05)) $pval.table         data1 data2 data3 data4 data5 data6 Fisher maxP p=0.001       12       4      698      180     1118       3    785   74 p=0.005       70      16     1430      572     1863   ...
metade written 2.1 years ago by lily10

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