User: Kasoji, Manjula NIH/NCI [C]

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Posts by Kasoji, Manjula NIH/NCI [C]

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Comment: C: in-group missing arrayQualityMetrics()
... Dear Wolfgang, I have figured out a workaround My dat seems to be a GeneFeatureSet object: > dat GeneFeatureSet (storageMode: lockedEnvironment) assayData: 1102500 features, 48 samples element names: exprs protocolData rowNames: 01_4T1_mouse1.CEL 02_4T1_mouse2.CEL ... 48_R3T_mouse4.CEL ...
written 3.8 years ago by Kasoji, Manjula NIH/NCI [C]120
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Answer: A: oligo read.celfiles() error
... Found the answer from a previous post: Try adding your AnnotatedDataFrame after creating the ExpressionFeatureSet: dat <- read.celfiles(list.celfiles()) phenoData(dat) <- pd My apologies for the redundant post. Thanks. On 1/14/14 3:45PM, "Guest [guest]" wrote: > >I'm having trou ...
written 3.8 years ago by Kasoji, Manjula NIH/NCI [C]120
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SeqGSEA estiGeneNBstat()
... Hi Xi, Thank you for your suggestion. I have pasted the information that you requested below. It seems testable is TRUE however Nbstat is FALSE for the the entire table. What should I do in this situation? > head(counts at featureData@data) exonIDs geneIDs te ...
seqgsea written 4.4 years ago by Kasoji, Manjula NIH/NCI [C]120 • updated 2.0 years ago by bojingjia20
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Comment: C: Sorting matrix by column
... Well, the fix was easy. I just did a no quote() on my matrix, and now I can order them and simply us the duplicated() function and it automatically removes the duplicates and keeps the one with the higher FC. Pasting an example below in case others want to view. :-) Thanks! > zz=z[order(z[,2]), ...
written 5.1 years ago by Kasoji, Manjula NIH/NCI [C]120
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Comment: C: Sorting matrix by column
... Thanks, guys. I think I got that because I did a cbind() with my ebayes() results and my annotation results from mget() that used to annotate my significant genes from the mogene10sttranscriptcluster db. I'll try out a few things. If you guys have any further suggestions or recommendations I will c ...
written 5.1 years ago by Kasoji, Manjula NIH/NCI [C]120
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Comment: C: Sorting matrix by column
... Hi Alex, Please see the output below: > str(x) List of 80 $ : chr "10371400" $ : chr "10453900" $ : chr "10375051" $ : chr "10575211" $ : chr "10566254" $ : chr "10602372" $ : chr "10398428" $ : chr "10383518" $ : chr "10397054" $ : chr "10384020" $ : chr "10608710" $ : chr "10363 ...
written 5.1 years ago by Kasoji, Manjula NIH/NCI [C]120
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Comment: C: Sorting matrix by column
... Ido not get anything: > orderVector1 Error: object 'orderVector1' not found On 10/23/12 11:42AM, "James W. MacDonald" wrote: >Also, what do you get from > >orderVector1 > > > >On 10/23/2012 11:38 AM, Kasoji, Manjula (NIH/NCI) [C] wrote: >> Hi Jim, >> >> ...
written 5.1 years ago by Kasoji, Manjula NIH/NCI [C]120
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Comment: C: Sorting matrix by column
... I get: > class(x) [1] "matrix" On 10/23/12 11:41AM, "James W. MacDonald" wrote: >What do you get from > >class(x) > >On 10/23/2012 11:38 AM, Kasoji, Manjula (NIH/NCI) [C] wrote: >> Hi Jim, >> >> The R session info below does correspond to the session I paste ...
written 5.1 years ago by Kasoji, Manjula NIH/NCI [C]120
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Comment: C: Sorting matrix by column
... Hi Jim, The R session info below does correspond to the session I pasted. When I tried your suggestion, I still get an error: > x[base::order(x[,2]),] Error in base::order(x[, 2]) : unimplemented type 'list' in 'orderVector1' I see that you don't have quotes around the ID and Gene Symbol na ...
written 5.1 years ago by Kasoji, Manjula NIH/NCI [C]120
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Comment: C: heatmap.2() get matrix after hierarchical clustering
... Hey, that's a pretty neat trick! I was going to use the reorder() function and re-order my input matrix based on the values returned by rowInd, but I think is may be more straightforward. Thank you Thomas and Jim! On 10/16/12 11:42AM, "Thomas Girke" wrote: >Try: > >## Some input sample ...
written 5.1 years ago by Kasoji, Manjula NIH/NCI [C]120

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