User: kritikamish99

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Posts by kritikamish99

<prev • 39 results • page 1 of 4 • next >
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Answer: A: design matrix problem im limma
... Hi newbie_R Can you show limma code (lmfit) which you used? ...
written 9 days ago by kritikamish9910
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Comment: C: How to filter all column using Loop
... Hi Martin Morgan I agree its not bioconductor questions. Actually i have Gene expression data . And it has 103 samples with FC value and 20000 probes What i wanted is filtering all sample at cut off 1.5 FC . So i queried here.     ...
written 9 days ago by kritikamish9910
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Comment: C: How to filter all column using Loop
... Hi Hauken_Heyken Thank you . The Code is working !! But its not giving me file b . Out result is the table "e" values also how will iterate for all the columns (file b and c ) ...
written 9 days ago by kritikamish9910
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Comment: C: How to filter all column using Loop
... Hi hauken_heyken my query is suppose i have table with column a , b, c ,d a=c("A","B","C","D","E","F","G") b=c(1,2,3,4,5,8,10) c=c(1,2,3,4,6,7,10) d=c(1,2,10,5,12,15,10) e = as.data.table(cbind(a,b,c,d))   What i want is 3 files with name b, c, d because its a column name. The file "b" wi ...
written 9 days ago by kritikamish9910
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How to filter all column using Loop
... I have 100 columns 1 column is name and 2 to 100 samples values I want to filter out column 2 to 100 with certain threshold say >=5 using loop. This will iterate for new file name corresponding to sample name. for example filtering value above 5 Col1 Col2 Col3 Col4 Col5 Col6 Col7 A 5 1 1 2 4 1 ...
filter loop written 10 days ago by kritikamish9910 • updated 9 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Tac and Bioconductor giving different results
... Hi Steve I was able to reproduce same results from both the methods Actually the out put file which i got from bioconductor was logged and TAC gives FC as unlogged after converting to antilog to my data i was able to get same results   ...
written 10 days ago by kritikamish9910
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Comment: C: Tac and Bioconductor giving different results
... Hi Steve I was performing u133a2 affymetrix gene expression study The normalisation method which i used was MAS5 After that i did FC calculation manually and then logFC manually too over exprs data that is eset i am getting different results compare to TACs . For example in column i am getting F ...
written 18 days ago by kritikamish9910
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Tac and Bioconductor giving different results
... Hi The questions may seem very general please bear! I have done analysis using TAC affymetrix software and bioconductor affy package the result are not showing similarity between both Which method i should go for TAC or Bioconductor ...
bioconductor results tac reproducbiltiy written 18 days ago by kritikamish9910 • updated 18 days ago by Steve Lianoglou12k
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Comment: C: mas5 normalisation giving negetive value after using exprs()
... Hi Gordon Exactly!!! This is for older affymetrix chip and they have different version of MAS5(prior was MAS4). But my exprs() is giving me negative value. not sure whether MAS5 is logged or MAS4 or earlier is unlogged!!!     ...
written 19 days ago by kritikamish9910
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Comment: C: mas5 normalisation giving negetive value after using exprs()
... Hi Gordon Can you give me any source that say MAS5 output is log-scale value As per my knowlegde MAS algorithm outputs the unlogged scale value ...
written 19 days ago by kritikamish9910

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Popular Question 11 months ago, created a question with more than 1,000 views. For how to use idat file for analyses in bioconductor

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