User: lily

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lily10
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Posts by lily

<prev • 21 results • page 1 of 3 • next >
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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 7 weeks 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 7 weeks ago by lily10 • updated 7 weeks ago by Aaron Lun17k
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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 8 weeks 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 8 weeks ago by lily10 • updated 8 weeks ago by Gordon Smyth32k
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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 10 weeks ago by lily10
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Comment: C: differentially expressed miRNA using edge R
... Thanks.  ...
written 11 weeks 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 11 weeks 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 11 weeks ago by lily10 • updated 11 weeks ago by Gordon Smyth32k
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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 13 months ago by lily10
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Comment: C: array Quality Metrics
... Thank you so much.. :-) ...
written 14 months ago by lily10

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