User: theobroma22

gravatar for theobroma22
theobroma2210
Reputation:
10
Status:
New User
Location:
Last seen:
9 months ago
Joined:
11 months, 4 weeks ago
Email:
t**********@gmail.com

Posts by theobroma22

<prev • 18 results • page 1 of 2 • next >
0
votes
1
answers
242
views
1
answers
Comment: C: Normalizing large scale RNA-seq datasets
... Yes, sva is appropriate and a great normalization tool. You can make contrasts in limma as well after sva normalization.  ...
written 9 months ago by theobroma2210
0
votes
2
answers
409
views
2
answers
Answer: A: log2 fold change in result of DEseq2
... Question: did you have technical replicates?? Those stats are quite odd.  ...
written 9 months ago by theobroma2210
0
votes
2
answers
281
views
2
answers
Answer: A: Possible approach of compare/interpret RNA-Seq results with microarray gene expr
... I would think that you have to convert the microarray data so that it's on the same scale as rna-seq data to compare the two, or vice-versa. Another way is to use pcr to validate the expressions of those 89 genes, or a subset of those at least, you observed in both sets. As such, right now you have ...
written 9 months ago by theobroma2210
0
votes
2
answers
341
views
2
answers
Answer: A: Unable to install scde in ubuntu 16.04 , this is what happens when I install scd
... Quit R and at the terminal command prompt write R CMD INSTALL scde. This is the same as using install.packages() in R. Did it work? ...
written 9 months ago by theobroma2210
0
votes
0
answers
279
views
0
answers
OmicCircos Error in Colnames attribute mus be the same length as the vector
... Dear Ying, I have my data.frame of 'karyotype' chromosomes: > par.chr    seg.name seg.Start   seg.End 1      mdm1         1  29289779 2      mdm2  29289779  65664585 3      mdm3  65664585  99375387 4      mdm4  99375387 122396126 5      mdm5 122396126 154003081 6      mdm6 154003081 179476216 7 ...
R omiccircos written 9 months ago by theobroma2210
0
votes
1
answers
274
views
1
answers
Comment: C: SPIA::spia function output
... Hi Adi, Thanks for the reply. I made the adjustments accordingly. However, I'm still getting an 'NA' for the pPERT value for Protein processing in the endoplasmic reticulum, which is now ranked as the top pathway. Please see below:     > head(cp_mean) #df of unique DEs with Q.Value < 0.05   ...
written 10 months ago by theobroma2210
0
votes
1
answers
232
views
1
answers
Comment: A: Probe sequences to Entrez Ids
... It's an apple fruit nimblegen array with little annotation. I have all of the array probe sequences, and files of the DE gene probe sets from a limma result. The ids use the contig number with a subsequent numerical code if such as Contig00001_2_f_100_1_200 which perhaps represents the nucleotide se ...
written 10 months ago by theobroma2210
0
votes
1
answer
232
views
1
answer
Probe sequences to Entrez Ids
... Is the a package, or a means by altering any usable package functions to get the Entrez IDs starting with a set of array probe sequences?  Thanks.  ...
R written 10 months ago by theobroma2210 • updated 10 months ago by Gordon Smyth32k
0
votes
2
answers
304
views
2
answers
Answer: A: Error: Pathway analysis using Sleuth results
... It seems the error is that your keggresids are not used as the keynames, or keys argument used to 'select' these from your object in order to map them to the pathway map. Can you label your arguments so that it's easier to read your code?  And did you forget to include the target_id column?    ...
written 10 months ago by theobroma2210
0
votes
1
answers
230
views
1
answers
Answer: A: Replacing values in an RleList
... Your code doesn't follow the logic for a list object. You need to provide some simulated data!! Lists can take the form of [x][[i]]. ...
written 10 months ago by theobroma2210

Latest awards to theobroma22

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 135 users visited in the last hour